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GitLab

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<h3>

Andreas Tille pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394">debb98f9</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-12-08T20:13:45Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.23+dfsg</pre>

</li>

</ul>

<h4>21 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#e352fc138c5e488dc34254c3ee2e99e3e9aaf288">

COPYRIGHT

</a>

</li>

<li class="file-stats">

<a href="#74b95601c3a6d9d565cd312fac64094ec0f9d847">

build.sbt

</a>

</li>

<li class="file-stats">

<a href="#59f81c123b3abbcb97274545796dd18706c3e106">

build.sh

</a>

</li>

<li class="file-stats">

<a href="#94cef6f41fc73ccebe945d2b889292615a09dddb">

project/plugins.sbt

</a>

</li>

<li class="file-stats">

<a href="#adac2c18d8a8d405c360c04a0da24090bf9a3402">

src/main/scala/org/broadinstitute/pilon/Assembler.scala

</a>

</li>

<li class="file-stats">

<a href="#63c81311ed6b4869429a1c7ae5408c74018ec324">

src/main/scala/org/broadinstitute/pilon/BamFile.scala

</a>

</li>

<li class="file-stats">

<a href="#9552dd85a8fb54c493222b18be6f38f666275239">

src/main/scala/org/broadinstitute/pilon/BaseSum.scala

</a>

</li>

<li class="file-stats">

<a href="#5e3fb33de64e26959d61ef889adc69cdd8994697">

src/main/scala/org/broadinstitute/pilon/Bases.scala

</a>

</li>

<li class="file-stats">

<a href="#64b7f895cb12140ceb6954c6b5ac6201d4f8fb70">

src/main/scala/org/broadinstitute/pilon/GapFiller.scala

</a>

</li>

<li class="file-stats">

<a href="#41fa529971dd7270998497c479f938d56c59e3ea">

src/main/scala/org/broadinstitute/pilon/GenomeFile.scala

</a>

</li>

<li class="file-stats">

<a href="#22c74dec22ce9a07c028f8ea0d3fa62179ca3f4f">

src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala

</a>

</li>

<li class="file-stats">

<a href="#1364bb1672cc9b5ea06d96a5f57e08c420f018db">

src/main/scala/org/broadinstitute/pilon/NormalDistribution.scala

</a>

</li>

<li class="file-stats">

<a href="#9301f94a8a30273eb398963b538f6f77373c915f">

src/main/scala/org/broadinstitute/pilon/PileUp.scala

</a>

</li>

<li class="file-stats">

<a href="#3fe73caca959968d50ca8052b982e85ac7cf08f2">

src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala

</a>

</li>

<li class="file-stats">

<a href="#b5368e22ab004e3abd523db7a2c70531cd4f1c46">

src/main/scala/org/broadinstitute/pilon/Pilon.scala

</a>

</li>

<li class="file-stats">

<a href="#2a148ba85fd1feca6ac26893fb76a27b151820d5">

src/main/scala/org/broadinstitute/pilon/Region.scala

</a>

</li>

<li class="file-stats">

<a href="#5d7fca8bf098e437cfd1a54fa348e3b22c998c41">

src/main/scala/org/broadinstitute/pilon/Scaffold.scala

</a>

</li>

<li class="file-stats">

<a href="#55b96fe7241a887a0773bd68059d930add258777">

src/main/scala/org/broadinstitute/pilon/Tracks.scala

</a>

</li>

<li class="file-stats">

<a href="#b86dfeb1da1963c17c8c21869c0c5c8f7ea18c87">

src/main/scala/org/broadinstitute/pilon/Utils.scala

</a>

</li>

<li class="file-stats">

<a href="#eb01396af0fb64925f2389164b4ca0c257ae7f11">

src/main/scala/org/broadinstitute/pilon/Vcf.scala

</a>

</li>

<li class="file-stats">

<a href="#85bba45a88212168f6b4f1a3b4368c4126f6a3e6">

src/main/scala/org/broadinstitute/pilon/Version.scala

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="e352fc138c5e488dc34254c3ee2e99e3e9aaf288">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#e352fc138c5e488dc34254c3ee2e99e3e9aaf288"><strong>COPYRIGHT</strong></a>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Copyright <span class="idiff left right">2012-2014</span> Broad Institute, Inc.</span>

</pre>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span>

</pre>

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2

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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">

2

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

<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Pilon is free software: you can redistribute it and/or modify</span>

</pre>

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<td class="diff-line-num old_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">

4

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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">

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">it under the terms of the GNU General Public License version 2</span>

</pre>

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</table>

<br>

</li>

<li id="74b95601c3a6d9d565cd312fac64094ec0f9d847">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#74b95601c3a6d9d565cd312fac64094ec0f9d847"><strong>build.sbt</strong></a>

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1

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<td class="diff-line-num new_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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">:=</span> <span class="s" style="color: #d14;">"pilon"</span></span>

</pre>

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2

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2

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

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

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="scala"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">:=</span> <span class="s" style="color: #d14;">"1.2<span class="idiff left right">2</span>"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="scala"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">:=</span> <span class="s" style="color: #d14;">"1.2<span class="idiff left right">3</span>"</span></span>

</pre>

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<td class="diff-line-num old_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">

4

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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">

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

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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="scala"><span class="n" style="color: #333;">scalaVersion</span> <span class="o" style="font-weight: 600;">:=</span> <span class="s" style="color: #d14;">"2.1<span class="idiff left right">1.8</span>"</span></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="scala"><span class="n" style="color: #333;">scalaVersion</span> <span class="o" style="font-weight: 600;">:=</span> <span class="s" style="color: #d14;">"2.1<span class="idiff left right">2.7</span>"</span></span>

</pre>

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="scala"><span class="n" style="color: #333;">scalacOptions</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"-deprecation"</span></span>

</pre>

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8

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8

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

</pre>

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

9

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9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="scala"><span class="n" style="color: #333;">scalacOptions</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"-feature"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="scala"><span class="nc" style="color: #458; font-weight: 600;">Seq</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">com</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">github</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">retronym</span><span class="o" style="font-weight: 600;">.</span><span class="nc" style="color: #458; font-weight: 600;">SbtOneJar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oneJarSettings</span><span class="k" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">_</span><span class="kt" style="color: #458; font-weight: 600;">*</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" 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">

12

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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC12" class="line" lang="scala"></span>

</pre>

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

13

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="scala"><span class="n" style="color: #333;">libraryDependencies</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"commons-lang"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">"commons-lang"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">"2.6"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="scala"></span></pre>

</td>

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</table>

<br>

</li>

<li id="59f81c123b3abbcb97274545796dd18706c3e106">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#59f81c123b3abbcb97274545796dd18706c3e106"><strong>build.sh</strong></a>

<hr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,6 @@ sed -e "s/\(date.*=\).*/\\1 \"$commitdate\"/" \</td>

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11

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell">    <span class="nt" style="color: navy;">-e</span> <span class="s2" style="color: #d14;">"s/</span><span class="se" style="color: #d14;">\(</span><span class="s2" style="color: #d14;">sbt.*=</span><span class="se" style="color: #d14;">\)</span><span class="s2" style="color: #d14;">.*/</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">1 </span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: teal;">$version</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">/"</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell">    <<span class="nv" style="color: teal;">$tmp</span> <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: teal;">$f</span></span>

</pre>

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

13

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

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#sbt $* package</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell">sbt <span class="nv" style="color: teal;">$*</span> <span class="idiff left right">one-jar</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: navy;">-sf</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/target/scala-2.1<span class="idiff left">1/pilon_2.11-</span><span class="nv" style="color: teal;"><span class="idiff">$version</span></span><span class="nt" style="color: navy;"><span class="idiff right">-one-jar</span></span>.jar ~/lib/pilon/pilon-dev.jar</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">sbt <span class="nv" style="color: teal;">$*</span> <span class="idiff left right">assembly</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: navy;">-sf</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/target/scala-2.1<span class="idiff left">2/pilon-assembly-</span><span class="nv" style="color: teal;"><span class="idiff right">$version</span></span>.jar ~/lib/pilon/pilon-dev.jar</span>

</pre>

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

16

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16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: teal;">$tmp</span> <span class="nv" style="color: teal;">$f</span></span></pre>

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</table>

<br>

</li>

<li id="94cef6f41fc73ccebe945d2b889292615a09dddb">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#94cef6f41fc73ccebe945d2b889292615a09dddb"><strong>project/plugins.sbt</strong></a>

<hr>

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<td class="diff-line-num old old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="scala"><span class="n" style="color: #333;">addSbtPlugin</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"com.<span class="idiff left">github.retronym"</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">"sbt-onejar"</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 right">"0.8</span>"</span><span class="o" style="font-weight: 600;">)</span></span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="scala"><span class="n" style="color: #333;">addSbtPlugin</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"com.<span class="idiff left">eed3si9n"</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">"sbt-assembly"</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 right">"0.14.6</span>"</span><span class="o" style="font-weight: 600;">)</span></span></pre>

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</li>

<li id="adac2c18d8a8d405c360c04a0da24090bf9a3402">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#adac2c18d8a8d405c360c04a0da24090bf9a3402"><strong>src/main/scala/org/broadinstitute/pilon/Assembler.scala</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</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">@@ -14,12 +14,11 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scala.annotation.tailrec</span></span>

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<td class="diff-line-num new_line old" data-linenumber="21" 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="LC21" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collection.JavaConversions._</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collection.mutable.</span><span class="o" style="font-weight: 600;">{</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Set</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">HashSet</span> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collection.mutable.</span><span class="o" style="font-weight: 600;">{</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">HashSet</span> <span class="o" style="font-weight: 600;">}</span></span>

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22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">htsjdk.samtools._</span></span>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="scala"><span class="k" style="font-weight: 600;">object</span> <span class="nc" style="color: #458; font-weight: 600;">Assembler</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<br>

</li>

<li id="63c81311ed6b4869429a1c7ae5408c74018ec324">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#63c81311ed6b4869429a1c7ae5408c74018ec324"><strong>src/main/scala/org/broadinstitute/pilon/BamFile.scala</strong></a>

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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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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2

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num old_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="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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

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

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5

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -14,13 +14,14 @@</td>

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collection.mutable.</span><span class="o" style="font-weight: 600;">{</span><span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;">,</span><span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="24" 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="LC23" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scala.collection.JavaConver<span class="idiff left right">sion</span>s._</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scala.collection.JavaConver<span class="idiff left right">ter</span>s._</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">htsjdk.samtools._</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="scala"><span class="k" style="font-weight: 600;">object</span> <span class="nc" style="color: #458; font-weight: 600;">BamFile</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" style="width: 35px; color: rgba(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">@@ -28,13 +29,23 @@ object BamFile {</td>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">maxInsertSizes</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;">((</span><span class="ss" style="color: #990073;">'frags </span><span class="o" style="font-weight: 600;">-></span> <span class="mi" style="color: #099;">500</span><span class="o" style="font-weight: 600;">),</span> <span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;">'jumps </span><span class="o" style="font-weight: 600;">-></span> <span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">),</span> <span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;">'unpaired </span><span class="o" style="font-weight: 600;">-></span> <span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">),</span> <span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;">'bam </span><span class="o" style="font-weight: 600;">-></span> <span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">))</span></span>

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">minOrientationPct</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">maxFragInsertSize</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">700</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="scala">  <span class="c1" style="color: #998; font-style: italic;">// long read type codes</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">notLongRead</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">nanoporeLongRead</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">pacbioLongRead</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="scala"><span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="38" 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="LC33" class="line" lang="scala"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BamFile</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">bamFile</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">bamType</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Symbol</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="scala"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BamFile</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">bamFile</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">bamType</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Symbol</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">val</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">subType</span></span><span class="k" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">Symbol</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff right">'none</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="scala">  <span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">BamFile._</span></span>

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

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">path</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamFile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getCanonicalPath</span><span class="o" style="font-weight: 600;">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">baseCount</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Long</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">longReadType</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;">'unpaired)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">subType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;">'nanopore)</span> <span class="n" style="color: #333;">nanoporeLongRead</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="scala">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">subType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;">'pacbio)</span> <span class="n" style="color: #333;">pacbioLongRead</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="scala">    <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="scala"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">reader</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">//val r = new SAMFileReader(bamFile, new File(path + BamFile.indexSuffix))</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">r</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">SamReaderFactory</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">makeDefault</span><span class="o" style="font-weight: 600;">().</span><span class="n" style="color: #333;">validationStringency</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ValidationStringency</span><span class="o" style="font-weight: 600;">.</span><span class="nc" style="color: #458; font-weight: 600;">SILENT</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">open</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamFile</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,7 +62,7 @@ class BamFile(val bamFile: File, var bamType: Symbol) {</td>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">getSeqs</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// returns an array of sequence records indexed by bam seq index</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">r</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="65" 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="LC54" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">seqs</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getFileHeader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getSequenceDictionary</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getSequences</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">seqs</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getFileHeader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getSequenceDictionary</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getSequences</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">asScala</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="scala">    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(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="LC67" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">seqArray</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">SAMSequenceRecord</span><span class="o" style="font-weight: 600;">](</span><span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">seqArray</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;">getSequenceIndex</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" style="width: 35px; color: rgba(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="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,7 +93,7 @@ class BamFile(val bamFile: File, var bamType: Symbol) {</td>

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="83" style="width: 35px; color: rgba(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="94" style="width: 35px; color: rgba(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="LC94" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">getUnaligned</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="95" style="width: 35px; color: rgba(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="LC95" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">r</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC85" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">queryUnmapped</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">validateRead</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">)).</span><span class="n" style="color: #333;">toList</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">queryUnmapped</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">asScala</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">filter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">validateRead</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">)).</span><span class="n" style="color: #333;">toList</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(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="97" style="width: 35px; color: rgba(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="LC97" class="line" lang="scala">    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(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="LC98" class="line" lang="scala">    <span class="n" style="color: #333;">reads</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(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="99" style="width: 35px; color: rgba(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="LC99" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,21 +101,21 @@ class BamFile(val bamFile: File, var bamType: Symbol) {</td>

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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(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="LC101" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">validateRead</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">SAMRecord</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="scala">    <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonPf</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getReadFailsVendorQualityCheckFlag</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="scala">      <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">duplicates</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getDuplicateReadFlag</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" 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">

93

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<td class="diff-line-num new_line old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC93" class="line" lang="scala">    <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left right">getNotPrimaryAlignmentFlag</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="scala">    <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left right">isSecondaryAlignment</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

95

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<td class="diff-line-num 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">

106

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

<pre style="margin: 0;"> <span id="LC106" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

96

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

107

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

<pre style="margin: 0;"> <span id="LC107" class="line" lang="scala">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

97

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

108

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">GenomeRegion</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">printInterval</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100000</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" 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">

98

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<td class="diff-line-num new_line old" data-linenumber="109" 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="LC98" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">pileUpRegion</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pileUpRegion</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

101

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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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

<pre style="margin: 0;"> <span id="LC111" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// Ugh. Is there a way for samtools to do the right thing here and get</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

102

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

112

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// the pairs for which only one end overlaps?  Adding 10k slop until</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

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<td class="diff-line-num new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

113

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// that's figured out.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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

<pre style="margin: 0;"> <span id="LC114" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">//pileUpRegion.addReads(bam.reader.queryOverlapping(name, start, stop))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">longRead</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;">'unpaired)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">subType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;">'nanopore </span><span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">subType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;">'pacbio)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<td class="diff-line-num new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

116

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

<pre style="margin: 0;"> <span id="LC116" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">r</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">queryOverlapping</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="scala">      <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">max</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">min</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="scala">      <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">max</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">10000</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">min</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contig</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">)<span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">asScala</span></span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">readsBefore</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pileUpRegion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readCount</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">baseCountBefore</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pileUpRegion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">baseCount</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">covBefore</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pileUpRegion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coverage</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">@@ -118,7 +129,7 @@ class BamFile(val bamFile: File, var bamType: Symbol) {</td>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="scala">        <span class="n" style="color: #333;">print</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;">lastLoc</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="scala">      <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">validateRead</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="132" 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="LC121" class="line" lang="scala">        <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">insertSize</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pileUpRegion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">addRead</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contigBases</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="scala">        <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">insertSize</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pileUpRegion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">addRead</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">contigBases</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">longReadType</span></span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="scala">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insertSize</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">huge</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(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="LC134" class="line" lang="scala">          <span class="c1" style="color: #998; font-style: italic;">//if (Pilon.debug) println("WARNING: huge insert " + insertSize + " " + read)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="scala">        <span class="o" style="font-weight: 600;">}</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="293" style="width: 35px; color: rgba(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">@@ -282,7 +293,7 @@ class BamFile(val bamFile: File, var bamType: Symbol) {</td>

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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">

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="scala">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="283" style="width: 35px; color: rgba(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="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">scan</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seqsOfInterest</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Set</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">])</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="284" style="width: 35px; color: rgba(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="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">r</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="296" 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="LC285" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">r</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">r</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 class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">asScala</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="286" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">validateRead</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">))</span> <span class="n" style="color: #333;">filtered</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="287" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="scala">      <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getReadUnmappedFlag</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">unmapped</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="288" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="scala">      <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="326" style="width: 35px; color: rgba(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="337" style="width: 35px; color: rgba(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">@@ -326,8 +337,8 @@ class BamFile(val bamFile: File, var bamType: Symbol) {</td>

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<td class="diff-line-num old_line" data-linenumber="326" style="width: 35px; color: rgba(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="337" style="width: 35px; color: rgba(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="LC337" class="line" lang="scala">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="327" style="width: 35px; color: rgba(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="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">readsInRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="328" style="width: 35px; color: rgba(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="339" style="width: 35px; color: rgba(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="LC339" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">r</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="340" 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="LC329" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">queryOverlapping</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">region</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;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">filter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">validateRead</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">)).</span><span class="n" style="color: #333;">toList</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="340" 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="LC330" class="line" lang="scala">    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); 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="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">queryOverlapping</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">region</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;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;"><span class="idiff left">asScala</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">filter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">validateRead</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">)).</span><span class="n" style="color: #333;">toList</span></span>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="scala">    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="o" style="font-weight: 600;"><span class="idiff left right">()</span></span></span>

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342

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

<pre style="margin: 0;"> <span id="LC342" class="line" lang="scala">    <span class="n" style="color: #333;">reads</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="332" style="width: 35px; color: rgba(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="LC343" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="333" style="width: 35px; color: rgba(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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344

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

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

</pre>

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<li id="9552dd85a8fb54c493222b18be6f38f666275239">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#9552dd85a8fb54c493222b18be6f38f666275239"><strong>src/main/scala/org/broadinstitute/pilon/BaseSum.scala</strong></a>

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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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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

2

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num old_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">

4

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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">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

</pre>

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

5

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5

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

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

16

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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

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

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

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

</pre>

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

19

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

</pre>

</td>

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<br>

</li>

<li id="5e3fb33de64e26959d61ef889adc69cdd8994697">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#5e3fb33de64e26959d61ef889adc69cdd8994697"><strong>src/main/scala/org/broadinstitute/pilon/Bases.scala</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -14,6 +14,7 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

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</li>

<li id="64b7f895cb12140ceb6954c6b5ac6201d4f8fb70">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#64b7f895cb12140ceb6954c6b5ac6201d4f8fb70"><strong>src/main/scala/org/broadinstitute/pilon/GapFiller.scala</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</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">@@ -14,11 +14,12 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

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

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<td class="diff-line-num old old_line" data-linenumber="21" 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="LC21" class="line" lang="scala"><span class="k" style="font-weight: 600;"><span class="idiff left">import</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff right">collection.JavaConversions._</span></span></span>

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

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collection.mutable.Map</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">htsjdk.samtools._</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,6 +49,8 @@ class GapFiller(val region: GenomeRegion) {</td>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">assembleAcrossBreak</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">break</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">isGap</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// TODO: ugh, this is ugly and really wants to be re-written.</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">//val reads = if (break.size < 100 && isGap) recruitLocalReads(break) else recruitReads(break)</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">//val longReads = recruitLongReads(break)</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">//if (Pilon.verbose) println("%d long reads".format(longReads.length))</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recruitReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">break</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="scala">    <span class="k" style="font-weight: 600;">var</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;">pathsFromLeft</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pathsFromRight</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">loop</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">assembleIntoBreak</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">break</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"L=%d R=%d"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pathsFromLeft</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pathsFromRight</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">))</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="360" style="width: 35px; color: rgba(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">@@ -360,17 +363,20 @@ class GapFiller(val region: GenomeRegion) {</td>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="scala">    <span class="n" style="color: #333;">minRadius</span> <span class="n" style="color: #333;">max</span> <span class="n" style="color: #333;">insertMean</span></span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="scala">    </span>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitReadsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bamType</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Symbol</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">bams</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamType</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitReadsFromBams</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bams</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">BamFile</span><span class="o" style="font-weight: 600;">])</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="scala">    <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">SAMRecord</span><span class="o" style="font-weight: 600;">]()</span></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">bams</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="scala">      <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">++=</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">recruitFlankReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">)</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">-<span id="LC370" class="line" lang="scala">      <span class="n" style="color: #333;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"# Recruiting <span class="idiff left">"</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">bamType</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</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 right">" reads</span>: count="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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371

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="scala">      <span class="n" style="color: #333;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"# Recruiting <span class="idiff left">reads from "</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">bams</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">toString</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 right">"</span>: count="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="scala">    <span class="n" style="color: #333;">reads</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="scala"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitReadsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bamType</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Symbol</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="scala">    <span class="n" style="color: #333;">recruitReadsFromBams</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamType</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="scala"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="scala">  <span class="c1" style="color: #998; font-style: italic;">//def recruitFrags(reg: Region) = mateMapOfType(reg, 'frags).values.toList</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitFrags</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recruitReadsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'frags)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="390" style="width: 35px; color: rgba(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">@@ -384,11 +390,18 @@ class GapFiller(val region: GenomeRegion) {</td>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="scala">    <span class="n" style="color: #333;">reads</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="scala"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitUnpaired</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recruitReadsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'unpaired)</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

393

</td>

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

<pre style="margin: 0;">+<span id="LC393" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitUnpaired</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

394

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

<pre style="margin: 0;">+<span id="LC394" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longread</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">recruitReadsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'unpaired)</span> <span class="k" style="font-weight: 600;">else</span> <span class="nc" style="color: #458; font-weight: 600;">Nil</span></span>

</pre>

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<td class="diff-line-num 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">

388

</td>

<td class="diff-line-num new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

395

</td>

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

<pre style="margin: 0;"> <span id="LC395" class="line" lang="scala"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

389

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<td class="diff-line-num new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

396

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

<pre style="margin: 0;"> <span id="LC396" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitLocalReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recruitFrags</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">++</span> <span class="n" style="color: #333;">recruitUnpaired</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

390

</td>

<td class="diff-line-num new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

397

</td>

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

<pre style="margin: 0;"> <span id="LC397" class="line" lang="scala"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

391

</td>

<td class="diff-line-num new_line old" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC391" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recruitLocalReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">++</span> <span class="n" style="color: #333;">recruitJumps</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

398

</td>

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

<pre style="margin: 0;">+<span id="LC398" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitLongReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

399

</td>

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

<pre style="margin: 0;">+<span id="LC399" class="line" lang="scala">    <span class="n" style="color: #333;">recruitReadsFromBams</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;">'unpaired)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longReadType</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>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

400

</td>

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

<pre style="margin: 0;">+<span id="LC400" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

401

</td>

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

<pre style="margin: 0;">+<span id="LC401" class="line" lang="scala"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

402

</td>

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

<pre style="margin: 0;">+<span id="LC402" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">recruitReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Region</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

403

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

<pre style="margin: 0;">+<span id="LC403" class="line" lang="scala">    <span class="n" style="color: #333;">recruitLocalReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">++</span> <span class="n" style="color: #333;">recruitJumps</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reg</span><span class="o" style="font-weight: 600;">)</span> <span class="c1" style="color: #998; font-style: italic;">// ++ recruitLongReads(reg)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

404

</td>

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

<pre style="margin: 0;">+<span id="LC404" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

392

</td>

<td class="diff-line-num new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

405

</td>

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

<pre style="margin: 0;"> <span id="LC405" class="line" lang="scala"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

393

</td>

<td class="diff-line-num new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

406

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

<pre style="margin: 0;"> <span id="LC406" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">writeBam</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fileName</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reads</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">SAMRecord</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>

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407

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fileName</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".sam"</span><span class="o" style="font-weight: 600;">)</span></span>

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<li id="41fa529971dd7270998497c479f938d56c59e3ea">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#41fa529971dd7270998497c479f938d56c59e3ea"><strong>src/main/scala/org/broadinstitute/pilon/GenomeFile.scala</strong></a>

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1

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<td class="diff-line-num new_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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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2

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

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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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num old_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">

4

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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">

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

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

5

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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14

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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

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

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

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

16

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

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

</pre>

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<br>

</li>

<li id="22c74dec22ce9a07c028f8ea0d3fa62179ca3f4f">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#22c74dec22ce9a07c028f8ea0d3fa62179ca3f4f"><strong>src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala</strong></a>

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1

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1

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,6 +46,7 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">ambiguous</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">](</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">changed</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">](</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">deleted</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">](</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">excluded</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">](</span><span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="scala">  <span class="c1" style="color: #998; font-style: italic;">//var lowCoverage = new Array[Boolean](size)</span></span>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="scala">  <span class="c1" style="color: #998; font-style: italic;">//var lowConfidence = new Array[Boolean](size)</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="scala"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,8 +133,17 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="scala">  <span class="c1" style="color: #998; font-style: italic;">//val bams = Map.empty[Symbol, BamRegion]</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">bams</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">BamFile</span><span class="o" style="font-weight: 600;">]()</span></span>

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

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamType</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Symbol</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bams</span> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">{</span> <span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bamType</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bamType</span> <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="scala"></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">nanoporeBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;">'unpaired)</span> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">{</span> <span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">subType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;">'nanopore}</span></span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="scala"></span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">pacbioBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;">'unpaired)</span> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">{</span> <span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">subType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;">'pacbio </span><span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="scala"></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">fragBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;">'frags)</span></span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="scala"></span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">longReadOnly</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fragBams</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isEmpty</span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">initializePileUps</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="scala">    <span class="n" style="color: #333;">pileUpRegion</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">PileUpRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">name</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;">stop</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -203,6 +214,8 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">meanCoverage</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pileUpRegion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">coverage</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(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="LC215" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">nReads</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pileUpRegion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readCount</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(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="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">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">longReadOnly</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">excludeMotifs</span><span class="o" style="font-weight: 600;">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="scala">    <span class="n" style="color: #333;">minDepth</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minDepth</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minDepth</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toInt</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="208" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="scala">      <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minDepth</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">meanCoverage</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">round</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toInt</span> <span class="n" style="color: #333;">max</span> <span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minMinDepth</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -247,7 +260,7 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>

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<td class="diff-line-num old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="scala">            <span class="n" style="color: #333;">deleted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

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<td class="diff-line-num old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="scala">            <span class="n" style="color: #333;">pileUpRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">deletions</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pu</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">deletions</span></span>

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<td class="diff-line-num new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="scala">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="263" 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="LC250" class="line" lang="scala">        <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="scala">        <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bc</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">score</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="scala">          <span class="c1" style="color: #998; font-style: italic;">// for ambiguous bases, fix them if --fix fixamb or if original base</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="scala">          <span class="c1" style="color: #998; font-style: italic;">// not one of the top two alternatives</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="scala">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">homo</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">addChange</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'snp,</span> <span class="n" style="color: #333;">pu</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" style="width: 35px; color: rgba(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">@@ -304,38 +317,41 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="scala">    <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">amb</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">changeList</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">kind</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pu</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">changeMap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">rBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refBase</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">loc</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">rBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refBase</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">bc</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pu</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">baseCall</span></span>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">cBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">base</span></span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="scala">      <span class="n" style="color: #333;">kind</span> <span class="k" style="font-weight: 600;">match</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="scala">        <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;">'snp </span><span class="k" style="font-weight: 600;">=></span></span>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="scala">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixSnps</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">snpFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="scala">          <span class="n" style="color: #333;">snps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="scala">        <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;">'amb </span><span class="k" style="font-weight: 600;">=></span></span>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="scala">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixSnps</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="316" 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">

316

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<td class="diff-line-num new_line old" data-linenumber="324" 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="LC316" class="line" lang="scala">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iupac</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

317

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<td class="diff-line-num new_line old" data-linenumber="324" 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="LC317" class="line" lang="scala">              <span class="c1" style="color: #998; font-style: italic;">// we put these on the small fix list because iupac codes can mess up assembly</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="318" 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">

318

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<td class="diff-line-num new_line old" data-linenumber="324" 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="LC318" class="line" lang="scala">              <span class="c1" style="color: #998; font-style: italic;">// flank anchor kmers</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="319" 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">

319

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<td class="diff-line-num new_line old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC319" class="line" lang="scala">              <span class="n" style="color: #333;">smallFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Bases</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toIUPAC</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cBase</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">altBase</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

320

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<td class="diff-line-num new_line old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC320" class="line" lang="scala">            <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="321" 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">

321

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<td class="diff-line-num new_line old" data-linenumber="324" 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="LC321" class="line" lang="scala">              <span class="n" style="color: #333;">snpFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

324

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">excluded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

325

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

<pre style="margin: 0;">+<span id="LC325" class="line" lang="scala">        <span class="n" style="color: #333;">kind</span> <span class="k" style="font-weight: 600;">match</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

326

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

<pre style="margin: 0;">+<span id="LC326" class="line" lang="scala">          <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;">'snp </span><span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

327

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

<pre style="margin: 0;">+<span id="LC327" class="line" lang="scala">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixSnps</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">snpFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

328

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

<pre style="margin: 0;">+<span id="LC328" class="line" lang="scala">            <span class="n" style="color: #333;">snps</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

329

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

<pre style="margin: 0;">+<span id="LC329" class="line" lang="scala">          <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;">'amb </span><span class="k" style="font-weight: 600;">=></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

330

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="scala">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixSnps</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longread</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

331

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

<pre style="margin: 0;">+<span id="LC331" class="line" lang="scala">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iupac</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

332

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="scala">                <span class="c1" style="color: #998; font-style: italic;">// we put these on the small fix list because iupac codes can mess up assembly</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="scala">                <span class="c1" style="color: #998; font-style: italic;">// flank anchor kmers</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="scala">                <span class="n" style="color: #333;">smallFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Bases</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toIUPAC</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cBase</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">altBase</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="scala">              <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="scala">                <span class="n" style="color: #333;">snpFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cBase</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toString</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="scala">              <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="scala">              <span class="n" style="color: #333;">amb</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="scala">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="323" 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="LC323" class="line" lang="scala">          <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="scala">          <span class="n" style="color: #333;">amb</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="scala">        <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;">'ins </span><span class="k" style="font-weight: 600;">=></span></span>

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="scala">          <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">insert</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insertion</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="scala">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixIndels</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">smallFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">insert</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="scala">          <span class="n" style="color: #333;">ins</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="scala">          <span class="n" style="color: #333;">insBases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">insert</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="scala">        <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;">'del </span><span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="scala">          <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">deletion</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">deletion</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="scala">          <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixIndels</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">smallFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">deletion</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>

</pre>

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333

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<td class="diff-line-num new_line old" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC333" class="line" lang="scala">          <span class="n" style="color: #333;">dels</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC334" class="line" lang="scala">          <span class="n" style="color: #333;">delBases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">deletion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC340" class="line" lang="scala">          <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;">'ins </span><span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC341" class="line" lang="scala">            <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">insert</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insertion</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC342" class="line" lang="scala">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixIndels</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">smallFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</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;">insert</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC343" class="line" lang="scala">            <span class="n" style="color: #333;">ins</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC344" class="line" lang="scala">            <span class="n" style="color: #333;">insBases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">insert</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC345" class="line" lang="scala">          <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;">'del </span><span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC346" class="line" lang="scala">            <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">deletion</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">deletion</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC347" class="line" lang="scala">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixIndels</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">smallFixList</span> <span class="o" style="font-weight: 600;">::=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">deletion</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>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC348" class="line" lang="scala">            <span class="n" style="color: #333;">dels</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC349" class="line" lang="scala">            <span class="n" style="color: #333;">delBases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">deletion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC350" class="line" lang="scala">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="335" style="width: 35px; color: rgba(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="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

351

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

<pre style="margin: 0;"> <span id="LC351" class="line" lang="scala">      <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="336" style="width: 35px; color: rgba(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="352" style="width: 35px; color: rgba(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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC352" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">logChange</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="337" style="width: 35px; color: rgba(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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC353" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="338" 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="LC338" class="line" lang="scala"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// Report some stats</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">nConfirmed</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">confirmed</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">=></span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">nonN</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">originalBases</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">=></span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'N'</span><span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="350" style="width: 35px; color: rgba(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="366" style="width: 35px; color: rgba(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">@@ -350,19 +366,19 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="ss" style="color: #990073;">'indels)</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"; corrected "</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"; found "</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="scala">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ins</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" small insertions totaling "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insBases</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" bases"</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="scala">    <span class="n" style="color: #333;">logln</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;">dels</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" small deletions totaling "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">delBases</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" bases"</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="scala"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// Report large collapsed regions (possible segmental duplication)</span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">duplications</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">duplicationEvents</span></span>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">duplications</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="scala">      <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">d</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">duplications</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">logln</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Large collapsed region: "</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="s" style="color: #d14;">" size "</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;">size</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="scala"><span class="idiff left right">    </span></span>

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360

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<td class="diff-line-num new_line old" data-linenumber="375" 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="LC360" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// Apply SNP fixes prior to reassemblies...it helps by giving better anchor sequence!<span class="idiff left right">  </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

375

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

376

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

<pre style="margin: 0;">+<span id="LC376" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// Apply SNP fixes prior to reassemblies...it helps by giving better anchor sequence!</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

361

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<td class="diff-line-num new_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

377

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// We can't change coords here, though, so no indels!</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

362

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<td class="diff-line-num new_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

378

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="scala">    <span class="n" style="color: #333;">fixIssues</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">snpFixList</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

363

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<td class="diff-line-num new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

379

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

364

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<td class="diff-line-num new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

380

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// Try to fill gaps</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="365" 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">

365

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<td class="diff-line-num new_line old" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="ss" style="color: #990073;">'gaps)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gaps</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left">length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

381

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="ss" style="color: #990073;">'gaps)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gaps</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;"><span class="idiff left right">nonEmpty</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

366

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<td class="diff-line-num new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

382

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

<pre style="margin: 0;"> <span id="LC382" class="line" lang="scala">      <span class="n" style="color: #333;">logln</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"# Attempting to fill gaps"</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

367

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<td class="diff-line-num new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

383

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

<pre style="margin: 0;"> <span id="LC383" class="line" lang="scala">      <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gap</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">gaps</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

368

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<td class="diff-line-num new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

384

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

<pre style="margin: 0;"> <span id="LC384" class="line" lang="scala">        <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">filler</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">GapFiller</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -376,7 +392,7 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>

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<td class="diff-line-num old_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

376

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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

392

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

<pre style="margin: 0;"> <span id="LC392" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

377

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<td class="diff-line-num new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

393

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// Try to reassemble around possible contiguity breaks, but stay away from gaps</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

394

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">breaks</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">possibleBreaks</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="379" 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">

379

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<td class="diff-line-num new_line old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC379" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="ss" style="color: #990073;">'local)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">breaks</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">is</span>Empty</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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395

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="ss" style="color: #990073;">'local)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">breaks</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">non</span>Empty</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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396

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="scala">      <span class="n" style="color: #333;">logln</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"# Attempting to fix local continuity breaks"</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

397

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="scala">      <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">break</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">breaks</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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382

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398

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="scala">        <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">filler</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">GapFiller</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="411" style="width: 35px; color: rgba(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">@@ -395,6 +411,37 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>

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411

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="scala">    <span class="n" style="color: #333;">fixIssues</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">smallFixList</span> <span class="o" style="font-weight: 600;">++</span> <span class="n" style="color: #333;">bigFixList</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

412

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

413

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

414

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">homoRun</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span><span class="o" style="font-weight: 600;">)</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

415

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">baseAtLoc</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">baseAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

416

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">loc</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">stop</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

417

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">baseAtLoc</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">loc</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

418

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

419

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="scala">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">loc</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

420

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

421

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="scala"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">nanoporeExclude</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

423

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="scala">    <span class="n" style="color: #333;">inRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">inRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

424

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

<pre style="margin: 0;">+<span id="LC424" class="line" lang="scala">      <span class="n" style="color: #333;">baseAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'C'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

425

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

<pre style="margin: 0;">+<span id="LC425" class="line" lang="scala">      <span class="n" style="color: #333;">baseAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'C'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

426

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

<pre style="margin: 0;">+<span id="LC426" class="line" lang="scala">      <span class="n" style="color: #333;">baseAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'G'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

427

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

<pre style="margin: 0;">+<span id="LC427" class="line" lang="scala">      <span class="n" style="color: #333;">baseAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'G'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

428

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

<pre style="margin: 0;">+<span id="LC428" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

429

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

<pre style="margin: 0;">+<span id="LC429" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

430

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

<pre style="margin: 0;">+<span id="LC430" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">excludeMotifs</span><span class="o" style="font-weight: 600;">()</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

431

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

<pre style="margin: 0;">+<span id="LC431" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">pb</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pacbioBams</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonEmpty</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

432

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

<pre style="margin: 0;">+<span id="LC432" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">nano</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nanoporeBams</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nonEmpty</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

433

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

<pre style="margin: 0;">+<span id="LC433" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">lr</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pb</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">nano</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

434

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

<pre style="margin: 0;">+<span id="LC434" class="line" lang="scala"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

435

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

<pre style="margin: 0;">+<span id="LC435" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;"><-</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">until</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

436

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

<pre style="margin: 0;">+<span id="LC436" class="line" lang="scala">      <span class="n" style="color: #333;">excluded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homoRun</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nano</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nanoporeExclude</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

437

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

<pre style="margin: 0;">+<span id="LC437" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="scala"></span>

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439

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">longReadChangeFilter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span><span class="o" style="font-weight: 600;">)</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Boolean</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

440

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">homoRun</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">)</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<td class="diff-line-num new old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

441

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="scala">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nanopore</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nanoporeExclude</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">)))</span> <span class="kc" style="font-weight: 600;">false</span></span>

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442

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="scala">    <span class="k" style="font-weight: 600;">else</span> <span class="kc" style="font-weight: 600;">true</span></span>

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443

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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444

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="scala"></span>

</pre>

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398

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445

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">reassemblyFixes</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">empty</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Region</span>, <span class="kt" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">]</span></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">closeCircle</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">estimatedLength</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<br>

</li>

<li id="1364bb1672cc9b5ea06d96a5f57e08c420f018db">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#1364bb1672cc9b5ea06d96a5f57e08c420f018db"><strong>src/main/scala/org/broadinstitute/pilon/NormalDistribution.scala</strong></a>

<hr>

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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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1

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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

2

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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num old_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">

4

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

</pre>

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

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -14,11 +14,11 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

15

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

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

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

16

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

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

17

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

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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

18

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

19

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

</pre>

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

19

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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21

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

</pre>

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

21

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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC21" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collection.mutable.ArrayBuffer</span></span>

</pre>

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22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math.pow</span></span>

</pre>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="scala"><span class="c1" style="color: #998; font-style: italic;">// Calculates the moments of a sample distribution.</span></span>

</pre>

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<br>

</li>

<li id="9301f94a8a30273eb398963b538f6f77373c915f">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#9301f94a8a30273eb398963b538f6f77373c915f"><strong>src/main/scala/org/broadinstitute/pilon/PileUp.scala</strong></a>

<hr>

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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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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

</pre>

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3

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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">

3

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num old_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">

4

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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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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

</pre>

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

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,8 +132,8 @@ class PileUp {</td>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="scala">  <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BaseCall</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">n</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseIndex</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">altBaseIndex</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">order</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">qualSum</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">order</span></span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="scala">      <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">order</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;">order</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))</span></span>

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<td class="diff-line-num new old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">order</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">qSum</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualSum</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">order</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">baseCount</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">order</span></span>

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<td class="diff-line-num new old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="scala">      <span class="idiff left right">  </span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">order</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;">order</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">base</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">indexBase</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseIndex</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="sc" style="color: #d14;">'N'</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">baseSum</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualSum</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sums</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseIndex</span><span class="o" style="font-weight: 600;">)</span></span>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,7 +144,7 @@ class PileUp {</td>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">homoScore</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">baseSum</span> <span class="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">baseSum</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">halfTotal</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">heteroScore</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">halfTotal</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">baseSum</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">abs</span> <span class="o" style="font-weight: 600;">-</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">halfTotal</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">altBaseSum</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">abs</span></span>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">homo</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">homoScore</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">heteroScore</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">homo</span> <span class="k" style="font-weight: 600;">=</span> <span class="cm" style="color: #998; font-style: italic;"><span class="idiff left">/* homoScore > 0 && */</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">homoScore</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">heteroScore</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">score</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mqSum</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">homoScore</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">heteroScore</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">abs</span>  <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">mqSum</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="scala">      <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">homo</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="180" style="width: 35px; color: rgba(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="181" style="width: 35px; color: rgba(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">@@ -180,12 +181,12 @@ class PileUp {</td>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="scala">    <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">insertCall</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insertions</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hetIndelCall</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insertionList</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">insPct</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insertions</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;"><span class="idiff left">2</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">insertions</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">deletions</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hetIndelCall</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insertionList</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">insPct</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="scala">      <span class="k" style="font-weight: 600;">else</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="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="scala"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="scala">    <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">deletionCall</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="189" 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="LC188" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">deletions</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hetIndelCall</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">deletionList</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delPct</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">deletions</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;"><span class="idiff left">2</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">deletions</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">insertions</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hetIndelCall</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">deletionList</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">delPct</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="scala">      <span class="k" style="font-weight: 600;">else</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="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="scala"></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>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -216,7 +217,7 @@ class PileUp {</td>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="scala">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indelStr</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getOrElse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indelStr</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="scala">      <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">winner</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sortBy</span><span class="o" style="font-weight: 600;">({</span> <span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_2</span> <span class="o" style="font-weight: 600;">}).</span><span class="n" style="color: #333;">last</span></span>

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<td class="diff-line-num new_line old" data-linenumber="220" 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="LC219" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">winner</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">indelList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</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="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">winner</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_2</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left">2</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">winner</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">indelList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</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="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">winStr</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">winner</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_1</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">winStr</span> <span class="n" style="color: #333;">contains</span> <span class="sc" style="color: #d14;">'N'</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</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="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

222

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<td class="diff-line-num new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

223

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">oldIndel</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<br>

</li>

<li id="3fe73caca959968d50ca8052b982e85ac7cf08f2">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#3fe73caca959968d50ca8052b982e85ac7cf08f2"><strong>src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala</strong></a>

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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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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

2

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num old_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">

4

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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">

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

</pre>

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

5

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,11 +14,12 @@</td>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

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

16

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

16

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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

19

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

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

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="22" 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="LC21" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scala.collection.JavaConver<span class="idiff left right">sion</span>s._</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scala.collection.JavaConver<span class="idiff left right">ter</span>s._</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC23" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">htsjdk.samtools._</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">Utils._</span></span>

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="scala"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(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="99" style="width: 35px; color: rgba(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">@@ -98,7 +99,7 @@ class PileUpRegion(name: String, start: Int, stop: Int)</td>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="scala">        <span class="n" style="color: #333;">pileups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">insertSize</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">pileups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">physCov</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="scala"></span>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">addRead</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">SAMRecord</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refBases</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Byte</span><span class="o" style="font-weight: 600;">])</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">addRead</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">SAMRecord</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refBases</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Byte</span><span class="o" style="font-weight: 600;">]<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">longRead</span></span><span class="k" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">Int</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">length</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getReadLength</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">bases</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getReadBases</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">mq</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getMappingQuality</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,12 +117,29 @@ class PileUpRegion(name: String, start: Int, stop: Int)</td>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="scala">    <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">baseString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bases</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Byte</span><span class="o" style="font-weight: 600;">])</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bases</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">{</span> <span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">toChar</span> <span class="o" style="font-weight: 600;">}</span> <span class="n" style="color: #333;">mkString</span> <span class="s" style="color: #d14;">""</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="scala">    <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">trusted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">offset</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">trustedFlank</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trustedFlank</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">offset</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="scala"></span>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">cigarElements</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getCigarElements</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

120

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="scala">    <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">homoRun</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i0</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span><span class="o" style="font-weight: 600;">)</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

121

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">baseAtLoc</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i0</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

122

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="scala">      <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">i0</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="n" style="color: #333;">until</span> <span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="scala">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">baseAtLoc</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

124

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="scala">      <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

125

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="scala">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

127

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="scala">    <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">nanoporeExclude</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i0</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="scala">      <span class="n" style="color: #333;">inRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i0</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">inRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i0</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="scala">        <span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i0</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'C'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

131

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="scala">        <span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i0</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'C'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

132

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="scala">        <span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i0</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'G'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

133

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="scala">        <span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i0</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'G'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

134

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="scala"></span>

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">cigarElements</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getCigarElements</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">asScala</span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// First count up number of clipped bases, so we can use to weight alignment</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">clippedBases</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cigarElements</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">e</span> <span class="k" style="font-weight: 600;">=></span> <span class="k" style="font-weight: 600;">if</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;">getOperator</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">CigarOperator</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;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLength</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">}).</span><span class="n" style="color: #333;">sum</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// de-rate mq proportionally to fraction of bases clipped</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">adjMq</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Utils</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">roundDiv</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">clippedBases</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">indelMq</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">longRead</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">adjMq</span> <span class="n" style="color: #333;">min</span> <span class="mi" style="color: #099;">8</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">adjMq</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// parse read alignment and add to pileups</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ele</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">cigarElements</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,7 +157,8 @@ class PileUpRegion(name: String, start: Int, stop: Int)</td>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="scala">              <span class="n" style="color: #333;">iloc</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="scala">              <span class="n" style="color: #333;">insertion</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insertion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">slice</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">++</span> <span class="n" style="color: #333;">insertion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">slice</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;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="scala">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="scala">            <span class="n" style="color: #333;">pileups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iloc</span><span class="o" style="font-weight: 600;">)).</span><span class="n" style="color: #333;">addInsertion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insertion</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readOffset</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">adjMq</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="scala">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!(</span><span class="n" style="color: #333;">longRead</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;">homoRun</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iloc</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="scala">              <span class="n" style="color: #333;">pileups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">iloc</span><span class="o" style="font-weight: 600;">)).</span><span class="n" style="color: #333;">addInsertion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insertion</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readOffset</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">indelMq</span><span class="o" style="font-weight: 600;">)</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">

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

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="scala">          <span class="o" style="font-weight: 600;">}</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">

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="scala">        <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;">CigarOperator</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">D</span> <span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="164" style="width: 35px; color: rgba(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="LC164" class="line" lang="scala">          <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">dloc</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locus</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -158,7 +177,9 @@ class PileUpRegion(name: String, start: Int, stop: Int)</td>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="scala">                  <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dloc</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">adjMq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">valid</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="scala">              <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(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="LC179" class="line" lang="scala">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="180" 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="LC161" class="line" lang="scala">            <span class="n" style="color: #333;">pileups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dloc</span><span class="o" style="font-weight: 600;">)).</span><span class="n" style="color: #333;">addDeletion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">slice</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dloc</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dloc</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readOffset</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">adjMq</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="scala">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!(</span><span class="n" style="color: #333;">longRead</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">homoRun</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dloc</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="scala">              <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">longRead</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">BamFile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nanoporeLongRead</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nanoporeExclude</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dloc</span><span class="o" style="font-weight: 600;">))))))</span></span>

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<td class="diff-line-num new old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="scala">              <span class="n" style="color: #333;">pileups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dloc</span><span class="o" style="font-weight: 600;">)).</span><span class="n" style="color: #333;">addDeletion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">slice</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dloc</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">dloc</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readOffset</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">indelMq</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="scala">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="scala">        <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;">CigarOperator</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">|</span> <span class="nc" style="color: #458; font-weight: 600;">CigarOperator</span><span class="o" style="font-weight: 600;">.</span><span class="nc" style="color: #458; font-weight: 600;">EQ</span> <span class="o" style="font-weight: 600;">|</span> <span class="nc" style="color: #458; font-weight: 600;">CigarOperator</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">X</span> <span class="k" style="font-weight: 600;">=></span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="scala">          <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;"><-</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">until</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,10 +187,8 @@ class PileUpRegion(name: String, start: Int, stop: Int)</td>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="scala">            <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trusted</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rOff</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="scala">              <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">locusPlus</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locus</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="scala">              <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">base</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rOff</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">toChar</span></span>

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="scala">              <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">qual</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rOff</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="scala">              <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">inRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locusPlus</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="scala">                <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locusPlus</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">adjMq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">valid</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="scala">              <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="scala">              <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">qual</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">longRead</span> <span class="o" style="font-weight: 600;">==</span> <span class="nc" style="color: #458; font-weight: 600;">BamFile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nanoporeLongRead</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nanoporeExclude</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locusPlus</span><span class="o" style="font-weight: 600;">)))</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">quals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rOff</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="scala">              <span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locusPlus</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">adjMq</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">valid</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="scala">            <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="scala">          <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="scala">        <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;">CigarOperator</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">S</span> <span class="k" style="font-weight: 600;">=></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">@@ -200,28 +219,10 @@ class PileUpRegion(name: String, start: Int, stop: Int)</td>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="scala">    <span class="n" style="color: #333;">physCovIncr</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">aStart</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">aEnd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">insert</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paired</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">valid</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="scala"></span>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">addReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reads</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">SAMRecordIterator</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refBases</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Byte</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">printInterval</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100000</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="scala">    <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">lastLoc</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">loc</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">addRead</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refBases</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">printInterval</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;">loc</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lastLoc</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">printInterval</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="scala">        <span class="n" style="color: #333;">lastLoc</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">printInterval</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">printInterval</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="scala">        <span class="n" style="color: #333;">print</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;">lastLoc</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="scala">      <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">dump</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;"><-</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pileups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="scala"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">callRegion</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;"><-</span> <span class="mi" style="color: #099;">0</span> <span class="n" style="color: #333;">until</span> <span class="n" style="color: #333;">size</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="scala">      <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">bc</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pileups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">).</span><span class="n" style="color: #333;">baseCall</span></span>

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<td class="diff-line-num new_line old" data-linenumber="226" 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="LC221" class="line" lang="scala">      <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">20</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">homo</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": bc="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" pu="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pileups</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">))</span></span>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">postProcess</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// To be called after all reads have been added to pileUps</span></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="scala">    <span class="n" style="color: #333;">computePhysCov</span></span>

</pre>

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<br>

</li>

<li id="b5368e22ab004e3abd523db7a2c70531cd4f1c46">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#b5368e22ab004e3abd523db7a2c70531cd4f1c46"><strong>src/main/scala/org/broadinstitute/pilon/Pilon.scala</strong></a>

<hr>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,7 +41,7 @@ object Pilon {</td>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">debug</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="scala">  <span class="c1" style="color: #998; font-style: italic;">// heuristics and control parameters</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">chunkSize</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000000</span></span>

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<td class="diff-line-num new_line old" data-linenumber="44" 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="LC43" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">defaultQual</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Byte</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1<span class="idiff left right">5</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">defaultQual</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Byte</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1<span class="idiff left right">0</span></span></span>

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

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">diploid</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">duplicates</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">dumpReads</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</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">@@ -56,16 +57,19 @@ object Pilon {</td>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">multiClosure</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">nonPf</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">oldIndel</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">longread</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">pacbio</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">nanopore</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">strays</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">threads</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">trSafe</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

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

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="scala">  <span class="c1" style="color: #998; font-style: italic;">// Global computed data</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">novelContigs</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">]()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="69" 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="LC65" class="line" lang="scala"><span class="idiff left right">  </span></span>

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

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="scala">  <span class="c1" style="color: #998; font-style: italic;">// for logging to output files</span></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="scala">  <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">commandArgs</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">]()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="scala"><span class="idiff left right">  </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="scala"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">main</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Array</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(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="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="scala">    <span class="n" style="color: #333;">commandArgs</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="scala">    <span class="n" style="color: #333;">println</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Version</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,7 +89,7 @@ object Pilon {</td>

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<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(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="LC89" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// Stray computation is expensive up front, so only turn it on</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(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="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="scala">    <span class="c1" style="color: #998; font-style: italic;">// if we're doing local reassembly</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="scala">    <span class="n" style="color: #333;">strays</span> <span class="o" style="font-weight: 600;">&=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="ss" style="color: #990073;">'gaps)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="ss" style="color: #990073;">'local)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="ss" style="color: #990073;">'scaffolds)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="92" 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="LC88" class="line" lang="scala"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(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="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamFiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(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="LC94" class="line" lang="scala">      <span class="n" style="color: #333;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="95" style="width: 35px; color: rgba(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="LC95" class="line" lang="scala">      <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exit</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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -100,11 +104,11 @@ object Pilon {</td>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(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="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="scala">    <span class="n" style="color: #333;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Fixing "</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">{</span><span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">}</span> <span class="n" style="color: #333;">mkString</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(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="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="scala">    <span class="n" style="color: #333;">genome</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">processRegions</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamFiles</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="107" 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="LC103" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tracks</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="scala">    <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tracks</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">tracks</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Tracks</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genome</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="scala">      <span class="n" style="color: #333;">tracks</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">standardTracks</span></span>

</pre>

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<td class="diff-line-num 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">

106

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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="scala">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

107

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<td class="diff-line-num new_line old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC107" class="line" lang="scala"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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

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

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

112

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

<pre style="margin: 0;"> <span id="LC112" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

113

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">optionParse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">list</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">])</span> <span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Unit</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="182" style="width: 35px; color: rgba(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="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">@@ -182,6 +186,14 @@ object Pilon {</td>

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<td class="diff-line-num old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

182

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="scala">      <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--multiclosure"</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">tail</span> <span class="k" style="font-weight: 600;">=></span>      <span class="c1" style="color: #998; font-style: italic;">// undocumented experimental option</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

183

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<td class="diff-line-num new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

187

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="scala">        <span class="n" style="color: #333;">multiClosure</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="scala">        <span class="n" style="color: #333;">optionParse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tail</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

189

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

<pre style="margin: 0;">+<span id="LC189" class="line" lang="scala">      <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--nanopore"</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">tail</span> <span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="scala">        <span class="n" style="color: #333;">bamFiles</span> <span class="o" style="font-weight: 600;">::=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">BamFile</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">),</span> <span class="ss" style="color: #990073;">'unpaired,</span> <span class="ss" style="color: #990073;">'nanopore)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="scala">        <span class="n" style="color: #333;">longread</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

192

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

<pre style="margin: 0;">+<span id="LC192" class="line" lang="scala">        <span class="n" style="color: #333;">nanopore</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="scala">        <span class="n" style="color: #333;">optionParse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tail</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="scala">      <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--nonpf"</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">tail</span> <span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

195

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="scala">        <span class="n" style="color: #333;">nonPf</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="scala">        <span class="n" style="color: #333;">optionParse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tail</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

185

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<td class="diff-line-num new_line" data-linenumber="197" style="width: 35px; color: rgba(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="LC197" class="line" lang="scala">      <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--oldindel"</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">tail</span> <span class="k" style="font-weight: 600;">=></span>      <span class="c1" style="color: #998; font-style: italic;">// undocumented experimental option</span></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="scala">        <span class="n" style="color: #333;">oldIndel</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="scala">        <span class="n" style="color: #333;">optionParse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tail</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -191,8 +203,10 @@ object Pilon {</td>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

191

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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">

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="scala">      <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--outdir"</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">tail</span> <span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="204" style="width: 35px; color: rgba(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="LC204" class="line" lang="scala">        <span class="n" style="color: #333;">outdir</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(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="LC205" class="line" lang="scala">        <span class="n" style="color: #333;">optionParse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tail</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="194" 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">

194

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<td class="diff-line-num new_line old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC194" class="line" lang="scala">      <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--nonpf"</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">tail</span> <span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="195" 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">

195

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<td class="diff-line-num new_line old" data-linenumber="206" 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="LC195" class="line" lang="scala">        <span class="n" style="color: #333;">nonPf</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

206

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="scala">      <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--pacbio"</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">tail</span> <span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

207

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="scala">        <span class="n" style="color: #333;">bamFiles</span> <span class="o" style="font-weight: 600;">::=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">BamFile</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">),</span> <span class="ss" style="color: #990073;">'unpaired,</span> <span class="ss" style="color: #990073;">'pacbio)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="scala">        <span class="n" style="color: #333;">longread</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

209

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="scala">        <span class="n" style="color: #333;">pacbio</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

196

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<td class="diff-line-num new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="scala">        <span class="n" style="color: #333;">optionParse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tail</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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<td class="diff-line-num new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="scala">      <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--targets"</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">::</span> <span class="n" style="color: #333;">tail</span> <span class="k" style="font-weight: 600;">=></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="scala">        <span class="n" style="color: #333;">targets</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="275" style="width: 35px; color: rgba(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">@@ -275,16 +289,16 @@ object Pilon {</td>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="scala">  </span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="scala">  <span class="c1" style="color: #998; font-style: italic;">// Ugly, but thank you http://stackoverflow.com/questions/17865823</span></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">setDefaultParallelism</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">numThreads</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span><span class="o" style="font-weight: 600;">)</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Unit</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="scala"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">parPkgObj</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scala</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">collection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parallel</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">`package`</span></span>

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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">

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="scala"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">defaultTaskSupportField</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parPkgObj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getClass</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getDeclaredFields</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="scala"><span class="idiff left right">         </span><span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"defaultTaskSupport"</span></span>

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<td class="diff-line-num old old_line" data-linenumber="281" 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="LC281" class="line" lang="scala"><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">}.</span><span class="n" style="color: #333;">get</span></span>

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<td class="diff-line-num new old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="scala"><span class="idiff left right">    </span><span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">parPkgObj</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scala</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">collection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parallel</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">`package`</span></span>

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<td class="diff-line-num new old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="scala"><span class="idiff left right">    </span><span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">defaultTaskSupportField</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parPkgObj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getClass</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getDeclaredFields</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="scala"><span class="idiff left right">      </span><span class="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"defaultTaskSupport"</span></span>

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<td class="diff-line-num new old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="scala"><span class="idiff left right">    </span><span class="o" style="font-weight: 600;">}.</span><span class="n" style="color: #333;">get</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="scala"></span>

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<td class="diff-line-num old old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="297" 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="LC283" class="line" lang="scala"><span class="idiff left right"> </span><span class="n" style="color: #333;">defaultTaskSupportField</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setAccessible</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="284" 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="LC284" class="line" lang="scala"><span class="idiff left right"> </span><span class="n" style="color: #333;">defaultTaskSupportField</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;">(</span></span>

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<td class="diff-line-num old old_line" data-linenumber="285" 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="LC285" class="line" lang="scala"><span class="idiff left">                       </span><span class="n" style="color: #333;"><span class="idiff">parPkgObj</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span></span>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="scala"><span class="idiff left right">                 </span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">scala</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">collection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parallel</span><span class="o" style="font-weight: 600;">.</span><span class="nc" style="color: #458; font-weight: 600;">ForkJoinTaskSupport</span><span class="o" style="font-weight: 600;">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="287" 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="LC287" class="line" lang="scala"><span class="idiff left right">                                 </span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">scala</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">concurrent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">forkjoin</span><span class="o" style="font-weight: 600;">.</span><span class="nc" style="color: #458; font-weight: 600;">ForkJoinPool</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">numThreads</span><span class="o" style="font-weight: 600;">)))</span></span>

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<td class="diff-line-num new old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="scala"><span class="idiff left right">    </span><span class="n" style="color: #333;">defaultTaskSupportField</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setAccessible</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="scala"><span class="idiff left right">    </span><span class="n" style="color: #333;">defaultTaskSupportField</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;">(</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="scala"><span class="idiff left">      </span><span class="n" style="color: #333;"><span class="idiff">parPkgObj</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">,</span></span></span>

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<td class="diff-line-num new old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="scala"><span class="idiff left right">      </span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">scala</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">collection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parallel</span><span class="o" style="font-weight: 600;">.</span><span class="nc" style="color: #458; font-weight: 600;">ForkJoinTaskSupport</span><span class="o" style="font-weight: 600;">(</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="scala"><span class="idiff left right">        </span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">scala</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">concurrent</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">forkjoin</span><span class="o" style="font-weight: 600;">.</span><span class="nc" style="color: #458; font-weight: 600;">ForkJoinPool</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">numThreads</span><span class="o" style="font-weight: 600;">)))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="scala">  <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="scala">  </span>

</pre>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="scala">  <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">usage</span> <span class="k" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="373" style="width: 35px; color: rgba(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="387" style="width: 35px; color: rgba(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">@@ -373,7 +387,7 @@ object Pilon {</td>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="scala"><span class="s" style="color: #d14;">              Print version string and exit.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="scala"><span class="s" style="color: #d14;">         HEURISTICS:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="scala"><span class="s" style="color: #d14;">           --defaultqual qual</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="scala"><span class="s" style="color: #d14;">              Assumes bases are of this quality if quals are no present in input BAMs (default 1<span class="idiff left right">5</span>).</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="scala"><span class="s" style="color: #d14;">              Assumes bases are of this quality if quals are no present in input BAMs (default 1<span class="idiff left right">0</span>).</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="377" style="width: 35px; color: rgba(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="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="scala"><span class="s" style="color: #d14;">           --flank nbases</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="scala"><span class="s" style="color: #d14;">              Controls how much of the well-aligned reads will be used; this many bases at each</span></span>

</pre>

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379

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="scala"><span class="s" style="color: #d14;">              end of the good reads will be ignored (default 10).</span></span>

</pre>

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<li id="2a148ba85fd1feca6ac26893fb76a27b151820d5">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#2a148ba85fd1feca6ac26893fb76a27b151820d5"><strong>src/main/scala/org/broadinstitute/pilon/Region.scala</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="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

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3

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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4

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -14,6 +14,7 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

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

16

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16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

</pre>

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</li>

<li id="5d7fca8bf098e437cfd1a54fa348e3b22c998c41">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#5d7fca8bf098e437cfd1a54fa348e3b22c998c41"><strong>src/main/scala/org/broadinstitute/pilon/Scaffold.scala</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

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3

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

</pre>

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

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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="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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

</pre>

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,8 +28,8 @@ package org.broadinstitute.pilon</td>

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="scala"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC30" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scala.collection.JavaConver<span class="idiff left right">sion</span>s._</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC31" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collection.mutable.</span><span class="o" style="font-weight: 600;">{</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Set</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff right">HashSet</span></span> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scala.collection.JavaConver<span class="idiff left right">ter</span>s._</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collection.mutable.</span><span class="o" style="font-weight: 600;">{</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span> <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(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="LC33" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">htsjdk.samtools._</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="scala"></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">@@ -347,7 +348,7 @@ object Scaffold {</td>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">reader</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reader</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="scala">    <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">eaList</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">EndAlignment</span><span class="o" style="font-weight: 600;">]</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Nil</span></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iterator</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getReadUnmappedFlag</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="scala">    <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">reader</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 class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">asScala</span></span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getReadUnmappedFlag</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">contig</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaffolds</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getReferenceIndex</span><span class="o" style="font-weight: 600;">())</span></span>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="scala">      <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">ca</span> <span class="k" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">EndAlignment</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">contig</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="scala">      <span class="c1" style="color: #998; font-style: italic;">//println(ca)</span></span>

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</li>

<li id="55b96fe7241a887a0773bd68059d930add258777">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#55b96fe7241a887a0773bd68059d930add258777"><strong>src/main/scala/org/broadinstitute/pilon/Tracks.scala</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -14,6 +14,7 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,9 +28,6 @@ package org.broadinstitute.pilon</td>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io._</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="scala"></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scala.collection.JavaConversions._</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="scala"><span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">htsjdk.samtools._</span></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="scala"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Tracks</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">reference</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">GenomeFile</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">standardTracks</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="scala">    <span class="n" style="color: #333;">makeBedTrack</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Pilon.bed"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Pilon"</span><span class="o" style="font-weight: 600;">)</span></span>

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</li>

<li id="b86dfeb1da1963c17c8c21869c0c5c8f7ea18c87">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#b86dfeb1da1963c17c8c21869c0c5c8f7ea18c87"><strong>src/main/scala/org/broadinstitute/pilon/Utils.scala</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</span></span>

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3

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num old_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">

4

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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">

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

</pre>

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

5

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

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

16

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

16

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

17

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

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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

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

19

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

</pre>

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

19

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

</pre>

</td>

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<br>

</li>

<li id="eb01396af0fb64925f2389164b4ca0c257ae7f11">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#eb01396af0fb64925f2389164b4ca0c257ae7f11"><strong>src/main/scala/org/broadinstitute/pilon/Vcf.scala</strong></a>

<hr>

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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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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

2

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num old_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">

4

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

</pre>

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

5

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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14

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

15

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

15

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

</td>

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

16

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

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</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">@@ -71,7 +72,8 @@ class Vcf(val file: File, val contigsWithSizes: List[(String, Int)] = Nil) {</td>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">close</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="scala"></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="scala">  <span class="k" style="font-weight: 600;">def</span> <span class="n" style="color: #333;">writeRecord</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">region</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">GenomeRegion</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">index</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Int</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="scala">      <span class="n" style="color: #333;">embedded</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Boolean</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">indelOk</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Boolean</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">)</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Unit</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="scala">                  <span class="n" style="color: #333;">embedded</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Boolean</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">indelOkArg</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Boolean</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">)</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Unit</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">indelOk</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indelOkArg</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">locus</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">locus</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">pileUp</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pileUpRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">)</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="scala">    <span class="k" style="font-weight: 600;">val</span> <span class="n" style="color: #333;">bc</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pileUp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">baseCall</span></span>

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<br>

</li>

<li id="85bba45a88212168f6b4f1a3b4368c4126f6a3e6">

<a href="https://salsa.debian.org/med-team/pilon/commit/debb98f957c35c9e47f4f20a0d26b0279554a394#85bba45a88212168f6b4f1a3b4368c4126f6a3e6"><strong>src/main/scala/org/broadinstitute/pilon/Version.scala</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">2012-2015</span> Broad Institute, Inc.</span></span>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * Copyright <span class="idiff left right">(c) 2012-2018</span> Broad Institute, Inc.</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="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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num old_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">

4

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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">

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Pilon.</span></span>

</pre>

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

5

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> * along with Pilon.  If not, see <http://www.gnu.org/licenses/>.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="scala"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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

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

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="scala"><span class="k" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">org.broadinstitute.pilon</span></span>

</pre>

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