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<h3>
Andreas Tille pushed to branch master
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/70bbfe31222b393a7de4c2ff3491f78747990f58">70bbfe31</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-02-04T22:54:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.24</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pilon/-/commit/1c82a6f35505976b8862867c13be4d8db28ca11d">1c82a6f3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-02-04T22:54:41+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pilon/-/commit/56f58c496c17d1ceea26f620ce97738c3dbfac6c">56f58c49</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-02-04T22:54:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.24'
Update to upstream version '1.24'
with Debian dir 8c3f397ea25b771347ee3cc0f6d91ed845499be3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pilon/-/commit/4b8359ec03af8333fa579fef248e56dea2f035e7">4b8359ec</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-02-04T22:54:42+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
</ul>
<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#74b95601c3a6d9d565cd312fac64094ec0f9d847">
build.sbt
</a>
</li>
<li class="file-stats">
<a href="#59f81c123b3abbcb97274545796dd18706c3e106">
build.sh
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</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#94cef6f41fc73ccebe945d2b889292615a09dddb">
project/plugins.sbt
</a>
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<li class="file-stats">
<a href="#63c81311ed6b4869429a1c7ae5408c74018ec324">
src/main/scala/org/broadinstitute/pilon/BamFile.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="#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="#5d7fca8bf098e437cfd1a54fa348e3b22c998c41">
src/main/scala/org/broadinstitute/pilon/Scaffold.scala
</a>
</li>
<li class="file-stats">
<a href="#eb01396af0fb64925f2389164b4ca0c257ae7f11">
src/main/scala/org/broadinstitute/pilon/Vcf.scala
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="74b95601c3a6d9d565cd312fac64094ec0f9d847">
<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#74b95601c3a6d9d565cd312fac64094ec0f9d847"><strong>build.sbt</strong></a>
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<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>
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="scala"></span>
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<td class="diff-line-num old old_line" data-linenumber="3" 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="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>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="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">4</span>"</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" 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">
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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>
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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">3.4</span>"</span></span>
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<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">
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<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>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="scala"></span>
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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>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="scala"></span>
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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>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="scala"></span></pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="scala"><span class="n" style="color: #333;">libraryDependencies</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"com.github.samtools"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">"htsjdk"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">"2.23.0"</span></span></pre>
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<li id="59f81c123b3abbcb97274545796dd18706c3e106">
<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#59f81c123b3abbcb97274545796dd18706c3e106"><strong>build.sh</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,5 +12,5 @@ sed -e "s/\(date.*=\).*/\\1 \"$commitdate\"/" \</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"> <<span class="nv" style="color: #008080;">$tmp</span> <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: #008080;">$f</span></span>
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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 $* package</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell">sbt <span class="nv" style="color: #008080;">$*</span> assembly</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-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 right">2</span>/pilon-assembly-<span class="nv" style="color: #008080;">$version</span>.jar ~/lib/pilon/pilon-dev.jar</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-sf</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/target/scala-2.1<span class="idiff left right">3</span>/pilon-assembly-<span class="nv" style="color: #008080;">$version</span>.jar ~/lib/pilon/pilon-dev.jar</span>
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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: #008080;">$tmp</span> <span class="nv" style="color: #008080;">$f</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pilon (1.24-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 04 Feb 2021 22:54:41 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">pilon (1.23+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> javahelper,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> scala,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libhtsjdk-java</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pilon</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pilon.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://github.com/broadinstitute/pilon/wiki</span>
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<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#94cef6f41fc73ccebe945d2b889292615a09dddb"><strong>project/plugins.sbt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="scala"><span class="nf" style="color: #900; font-weight: 600;">addSbtPlugin</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"com.eed3si9n"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">"sbt-assembly"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">"0.1<span class="idiff left right">4.6</span>"</span><span class="o" style="font-weight: 600;">)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="scala"><span class="nf" style="color: #900; font-weight: 600;">addSbtPlugin</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"com.eed3si9n"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">"sbt-assembly"</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">"0.1<span class="idiff left right">5.0</span>"</span><span class="o" style="font-weight: 600;">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#63c81311ed6b4869429a1c7ae5408c74018ec324"><strong>src/main/scala/org/broadinstitute/pilon/BamFile.scala</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,12 +21,12 @@ package org.broadinstitute.pilon</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="scala"></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;">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>
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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.<span class="idiff left right">collection.Java</span>Converters._</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;">scala.<span class="idiff left right">jdk.Collection</span>Converters._</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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<pre style="margin: 0;"> <span id="LC26" class="line" lang="scala"></span>
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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>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">indexSuffix</span> <span class="k" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">".bai"</span></span>
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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="nv" style="color: #008080;">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;"><span class="idiff left">'frags</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">500</span></span><span class="o" style="font-weight: 600;"><span class="idiff">),</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="ss" style="color: #990073;"><span class="idiff">'jumps</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">10000</span></span><span class="o" style="font-weight: 600;"><span class="idiff">),</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="ss" style="color: #990073;"><span class="idiff">'unpaired</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">10000</span></span><span class="o" style="font-weight: 600;"><span class="idiff">),</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="ss" style="color: #990073;"><span class="idiff right">'bam</span></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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<pre style="margin: 0;">+<span id="LC29" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">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="s" style="color: #d14;"><span class="idiff left">"frags"</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">500</span></span><span class="o" style="font-weight: 600;"><span class="idiff">),</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"jumps"</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">10000</span></span><span class="o" style="font-weight: 600;"><span class="idiff">),</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"unpaired"</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">10000</span></span><span class="o" style="font-weight: 600;"><span class="idiff">),</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"bam"</span></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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<pre style="margin: 0;"> <span id="LC30" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">minOrientationPct</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span></span>
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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="nv" style="color: #008080;">maxFragInsertSize</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">700</span></span>
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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>
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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">@@ -35,14 +35,14 @@ object BamFile {</td>
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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="nv" style="color: #008080;">pacbioLongRead</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="scala"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="scala"></span>
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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="nv" style="color: #008080;">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;">S<span class="idiff left">ymbol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</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="nv" style="color: #008080;"><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 class="o" style="font-weight: 600;">{</span></span>
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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="nv" style="color: #008080;">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;">S<span class="idiff left">tring</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</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="nv" style="color: #008080;"><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">String</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">"none"</span></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="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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<pre style="margin: 0;"> <span id="LC40" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">path</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bamFile</span><span class="o" style="font-weight: 600;">.</span><span class="py">getCanonicalPath</span><span class="o" style="font-weight: 600;">()</span></span>
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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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<pre style="margin: 0;"> <span id="LC42" class="line" lang="scala"></span>
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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="nv" style="color: #008080;">longReadType</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; 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;"><span class="idiff left right">'unpaired</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="scala"> <span class="nf" style="color: #900; 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;"><span class="idiff left right">'nanopore</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">nanoporeLongRead</span></span>
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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="nf" style="color: #900; 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;"><span class="idiff left right">'pacbio</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">pacbioLongRead</span></span>
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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="nv" style="color: #008080;">longReadType</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; 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="s" style="color: #d14;"><span class="idiff left right">"unpaired"</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="scala"> <span class="nf" style="color: #900; 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="s" style="color: #d14;"><span class="idiff left right">"nanopore"</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">nanoporeLongRead</span></span>
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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="nf" style="color: #900; 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="s" style="color: #d14;"><span class="idiff left right">"pacbio"</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">pacbioLongRead</span></span>
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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>
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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>
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<pre style="margin: 0;"> <span id="LC48" 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">@@ -75,7 +75,7 @@ class BamFile(val bamFile: File, var bamType: Symbol, val subType: Symbol = 'non</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="scala"> <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>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">validateSeqs</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>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">require</span><span class="o" style="font-weight: 600;">(<span class="idiff left">!</span></span><span class="nv" style="color: #008080;"><span class="idiff">getSeqNames</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">intersect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seqsOfInterest</span></span><span class="o" style="font-weight: 600;"><span class="idiff">).</span></span><span class="py"><span class="idiff">isEmpty</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bamFile</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" doesn't have sequence for any of "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">seqsOfInterest</span><span class="o" style="font-weight: 600;">.</span><span class="py">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>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">require</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;"><span class="idiff left">getSeqNames</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">intersect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seqsOfInterest</span></span><span class="o" style="font-weight: 600;"><span class="idiff">).</span></span><span class="py"><span class="idiff">nonEmpty</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">bamFile</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">toString</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" doesn't have sequence for any of "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">seqsOfInterest</span><span class="o" style="font-weight: 600;">.</span><span class="py">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>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="scala"></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -112,7 +112,8 @@ class BamFile(val bamFile: File, var bamType: Symbol, val subType: Symbol = 'non</td>
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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>
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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>
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<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>
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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="nv" style="color: #008080;">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="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 class="o" style="font-weight: 600;">)</span></span>
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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="nv" style="color: #008080;">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="s" style="color: #d14;">"unpaired"</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">subType</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"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="s" style="color: #d14;">"pacbio"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="scala"></span>
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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="nv" style="color: #008080;">r</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">queryOverlapping</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">name</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="scala"> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">contig</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span><span class="o" style="font-weight: 600;">).</span><span class="py">asScala</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -272,22 +273,22 @@ class BamFile(val bamFile: File, var bamType: Symbol, val subType: Symbol = 'non</td>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">nStrays</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">pairs</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">nStrays</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">pairs</span><span class="o" style="font-weight: 600;"><span class="idiff left right">()</span>.</span><span class="py">length</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printDebug</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"mm: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">readMap1</span><span class="o" style="font-weight: 600;">.</span><span class="py">size</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="nv" style="color: #008080;">readMap2</span><span class="o" style="font-weight: 600;">.</span><span class="py">size</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;">nStrays</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>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="scala"> <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>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">strayMateMap</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;">MateMap</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">autoBam</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;">S<span class="idiff left right">ymbol</span></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="LC283" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">autoBam</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;">S<span class="idiff left right">tring</span></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="LC284" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fr</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pctFR</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">rf</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pctRF</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">un</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pctUnpaired</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">un</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">fr</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">un</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">rf</span><span class="o" style="font-weight: 600;">)</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'unpaired</span></span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">un</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">fr</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">un</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">rf</span><span class="o" style="font-weight: 600;">)</span> <span class="s" style="color: #d14;"><span class="idiff left right">"unpaired"</span></span></span>
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<pre style="margin: 0;"> <span id="LC289" 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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<pre style="margin: 0;"> <span id="LC290" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">insertSize</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rf</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fr</span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;">insertStatsRF</span><span class="o" style="font-weight: 600;">.</span><span class="py">mean</span> <span class="k" style="font-weight: 600;">else</span> <span class="nv" style="color: #008080;">insertStatsFR</span><span class="o" style="font-weight: 600;">.</span><span class="py">mean</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="scala"> <span class="nf" style="color: #900; 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;">maxFragInsertSize</span><span class="o" style="font-weight: 600;">)</span> <span class="ss" style="color: #990073;"><span class="idiff left">'jumps</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="ss" style="color: #990073;"><span class="idiff right">'frags</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="scala"> <span class="nf" style="color: #900; 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;">maxFragInsertSize</span><span class="o" style="font-weight: 600;">)</span> <span class="s" style="color: #d14;"><span class="idiff left">"jumps"</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="s" style="color: #d14;"><span class="idiff right">"frags"</span></span></span>
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291
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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292
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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293
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="scala"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,7 +319,7 @@ class BamFile(val bamFile: File, var bamType: Symbol, val subType: Symbol = 'non</td>
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318
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="scala"> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">close</span></span>
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319
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="scala"></span>
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320
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321
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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="nv" style="color: #008080;">totalReads</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapped</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="n" style="color: #333;">filtered</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">summary</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="s" style="color: #d14;">": %d reads, %d filtered, %d mapped, %d proper"</span><span class="o" style="font-weight: 600;">.</span><span class="py">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">totalReads</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="n" style="color: #333;">mapped</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">proper</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;">var</span> <span class="n" style="color: #333;">summary</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bamFile</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="py"><span class="idiff right">toString</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": %d reads, %d filtered, %d mapped, %d proper"</span><span class="o" style="font-weight: 600;">.</span><span class="py">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">totalReads</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="n" style="color: #333;">mapped</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">proper</span><span class="o" style="font-weight: 600;">)</span></span>
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322
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">strays</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">summary</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="nv" style="color: #008080;">strayMateMap</span><span class="o" style="font-weight: 600;">.</span><span class="py">nStrays</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" stray"</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">insertCount</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">insertStatsFR</span><span class="o" style="font-weight: 600;">.</span><span class="py">count</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">insertStatsRF</span><span class="o" style="font-weight: 600;">.</span><span class="py">count</span></span>
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pctFR</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minOrientationPct</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="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -328,9 +329,9 @@ class BamFile(val bamFile: File, var bamType: Symbol, val subType: Symbol = 'non</td>
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328
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pctUnpaired</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minOrientationPct</span><span class="o" style="font-weight: 600;">)</span></span>
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329
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="scala"> <span class="n" style="color: #333;">summary</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">", Unpaired "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pctUnpaired</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;">insertStatsUnpaired</span></span>
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330
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="scala"> <span class="n" style="color: #333;">summary</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">", max "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">maxInsertSize</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="scala"> <span class="nf" style="color: #900; 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;"><span class="idiff left right">'bam</span></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="LC332" class="line" lang="scala"> <span class="n" style="color: #333;">bamType</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">autoBam</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="scala"> <span class="n" style="color: #333;">summary</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="nv" style="color: #008080;">bamType</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="py"><span class="idiff right">name</span></span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="scala"> <span class="nf" style="color: #900; 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="s" style="color: #d14;"><span class="idiff left right">"bam"</span></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="LC333" class="line" lang="scala"> <span class="n" style="color: #333;">bamType</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">autoBam</span><span class="o" style="font-weight: 600;"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="scala"> <span class="n" style="color: #333;">summary</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;">bamType</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">summary</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC337" 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 new_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -346,7 +347,7 @@ class BamFile(val bamFile: File, var bamType: Symbol, val subType: Symbol = 'non</td>
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346
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">flanks</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">flankRegion</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>
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347
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348
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<pre style="margin: 0;"> <span id="LC348" 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="nf" style="color: #900; font-weight: 600;">readsInRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">flanks</span><span class="o" style="font-weight: 600;">)</span> </span>
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348
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"readsInRegion flanks: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">flanks</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="nv" style="color: #008080;">reads</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" reads"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">strays</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;"><span class="idiff left right">'unpaired</span></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="LC350" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">strays</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="s" style="color: #d14;"><span class="idiff left right">"unpaired"</span></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="LC351" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">mm</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;">MateMap</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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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;">mm</span><span class="o" style="font-weight: 600;">.</span><span class="py">printDebug</span></span>
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="scala"> <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">++=</span> <span class="nv" style="color: #008080;">mm</span><span class="o" style="font-weight: 600;">.</span><span class="py">findStrays</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">@@ -377,7 +378,7 @@ class BamFile(val bamFile: File, var bamType: Symbol, val subType: Symbol = 'non</td>
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377
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">frPct</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pctFR</span></span>
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378
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="scala"></span>
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379
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">mates</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="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Nil</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;"><-</span> <span class="nv" style="color: #008080;">mateMap</span><span class="o" style="font-weight: 600;">.</span><span class="py">pairs</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="LC381" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;"><-</span> <span class="nv" style="color: #008080;">mateMap</span><span class="o" style="font-weight: 600;">.</span><span class="py">pairs</span><span class="o" style="font-weight: 600;"><span class="idiff left right">()</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>
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381
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!(</span><span class="nv" style="color: #008080;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="py">getReadUnmappedFlag</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="py">getProperPairFlag</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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<pre style="margin: 0;"> <span id="LC383" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">rc</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="py">getReadNegativeStrandFlag</span></span>
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383
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">start</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="py">getAlignmentStart</span></span>
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<li id="64b7f895cb12140ceb6954c6b5ac6201d4f8fb70">
<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#64b7f895cb12140ceb6954c6b5ac6201d4f8fb70"><strong>src/main/scala/org/broadinstitute/pilon/GapFiller.scala</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,7 +73,7 @@ class GapFiller(val region: GenomeRegion) {</td>
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Gap closed but bad size: "</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">closedLength</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">solutionOK</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">solution</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isGap</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(<span class="idiff left">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixList</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff">'breaks</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">loop</span><span class="o" style="font-weight: 600;">.</span><span class="py">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>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isGap</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;"><span class="idiff left">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">fixBreaks</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">loop</span><span class="o" style="font-weight: 600;">.</span><span class="py">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>
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// build partial solution using consensus from each side, opening gap if necessary</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="nv" style="color: #008080;">fromRight</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">consensusFromRight</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>
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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="nv" style="color: #008080;">fromLeft</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">consensusFromLeft</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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -127,12 +127,10 @@ class GapFiller(val region: GenomeRegion) {</td>
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="scala"> <span class="nv" style="color: #008080;">assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">addReads</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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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">dumpReads</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">writeBam</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">break</span><span class="o" style="font-weight: 600;">.</span><span class="py">toString</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="LC129" class="line" lang="scala"> <span class="nv" style="color: #008080;">assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">buildGraph</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">contains</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="ss" style="color: #990073;"><span class="idiff">'novel</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">novelContigs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">Nil</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="LC130" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">Novel</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">novelContigs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nc" style="color: #458; font-weight: 600;">Nil</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="LC131" class="line" lang="scala"> <span class="nv" style="color: #008080;">assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">addGraphSeqs</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">novelContigs</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="scala"> <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="LC132" class="line" lang="scala"> <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="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">assembler</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>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//if (Pilon.fixList contains 'novelbreaks) assembler.novel</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="scala"></span>
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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="nv" style="color: #008080;">startOffset</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">breakRadius</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">start</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">break</span><span class="o" style="font-weight: 600;">.</span><span class="py">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">startOffset</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">max</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">start</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">@@ -169,22 +167,22 @@ class GapFiller(val region: GenomeRegion) {</td>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="scala"> <span class="n" style="color: #333;">solutionSet</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="scala"> <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="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">val</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">solutions</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">solutionSet</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">toList</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sortWith</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">{</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">b</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">_3</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">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="nv" style="color: #008080;"><span class="idiff">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">_2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">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="nv" style="color: #008080;"><span class="idiff">b</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">_3</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">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="nv" style="color: #008080;"><span class="idiff">b</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">_2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="scala"> <span class="k" style="font-weight: 600;">va<span class="idiff left">r</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">solutionLengths</span></span><span class="idiff"> </span><span class="k" 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">Set</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">Int</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]()</span></span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="scala"> <span class="n" style="color: #333;"><span class="idiff left">solutions</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">map</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">s</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">solutionLengths</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+=</span></span> <span class="nv" style="color: #008080;">s</span><span class="o" style="font-weight: 600;">.</span><span class="py">_3</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">s</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</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>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="scala"> <span class="k" style="font-weight: 600;">va<span class="idiff left">l</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">solutions</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">solutionSet</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">toList</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sortWith</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">{</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">b</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">_3</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">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="nv" style="color: #008080;"><span class="idiff">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">_2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">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="nv" style="color: #008080;"><span class="idiff">b</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">_3</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">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="nv" style="color: #008080;"><span class="idiff">b</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">_2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">}</span></span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="scala"> <span class="k" style="font-weight: 600;"><span class="idiff left">var</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">solutionLengths</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">solutionSet</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">map</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">s</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">=></span></span> <span class="nv" style="color: #008080;">s</span><span class="o" style="font-weight: 600;">.</span><span class="py">_3</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">s</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span><span class="o" style="font-weight: 600;">}</span></span>
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175
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="scala"></span>
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176
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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177
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"breakJoins: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">solutions</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" solutions; lengths "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">solutionLengths</span><span class="o" style="font-weight: 600;">)</span></span>
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178
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="scala"> <span class="nf" style="color: #900; 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;">solutions</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</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;">s</span><span class="o" style="font-weight: 600;">)</span></span>
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179
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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180
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">solutionLengths</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="o" style="font-weight: 600;">{</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"...all solutions of same length, using <span class="idiff left right">first</span> above"</span><span class="o" style="font-weight: 600;">)</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"...all solutions of same length, using <span class="idiff left right">smallest total change</span> above"</span><span class="o" style="font-weight: 600;">)</span></span>
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182
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="scala"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">solutions</span><span class="o" style="font-weight: 600;">.</span><span class="py">head</span><span class="o" style="font-weight: 600;">)</span></span>
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183
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181
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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="k" style="font-weight: 600;">else</span><span class="o" style="font-weight: 600;">{</span></span>
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184
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="scala"> <span class="n" style="color: #333;">solutions</span></span>
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185
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183
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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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="scala"><span class="idiff left right"> </span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="scala"></span>
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188
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">joinBreak</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">startArg</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="n" style="color: #333;">forward</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;">reverse</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;">stopArg</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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189
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">start</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startArg</span></span>
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190
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">stop</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stopArg</span></span>
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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="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -203,13 +201,13 @@ class GapFiller(val region: GenomeRegion) {</td>
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203
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">patch</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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204
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">solution</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">trimPatch</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;">patch</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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205
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="scala"> <span class="n" style="color: #333;">start</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="py">_1</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="scala"><span class="idiff left right"> </span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="scala"></span>
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207
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span> <span class="o" style="font-weight: 600;">==</span> <span class="nv" style="color: #008080;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="py">_3</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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208
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"...no change"</span><span class="o" style="font-weight: 600;">)</span></span>
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209
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="scala"> <span class="n" style="color: #333;">solution</span></span>
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210
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208
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<pre style="margin: 0;"> <span id="LC208" 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>
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211
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"...start="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" ref=("</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</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="nv" style="color: #008080;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span><span class="idiff left right"> </span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"...start="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" ref=("</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</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="nv" style="color: #008080;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span></span>
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213
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="scala"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" new=("</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="py">_3</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</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="nv" style="color: #008080;">solution</span><span class="o" style="font-weight: 600;">.</span><span class="py">_3</span><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="n" style="color: #333;">solution</span></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="scala"> <span class="o" 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">@@ -218,7 +216,7 @@ class GapFiller(val region: GenomeRegion) {</td>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="scala"> <span class="n" style="color: #333;">noSolution</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</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>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="scala"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">properOverlap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">left</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;">right</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;">minOverlap</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;">String</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="LC221" 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="nf" style="color: #900; font-weight: 600;">substrMatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</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;">aOffset</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="n" style="color: #333;">b</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;">bOffset</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="n" style="color: #333;">len</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -304,7 +302,7 @@ class GapFiller(val region: GenomeRegion) {</td>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">estimatedLength</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="LC303" class="line" lang="scala"> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">recruitReads</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>
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<pre style="margin: 0;"> <span id="LC304" 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>
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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="nv" style="color: #008080;">unpairedBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;"><span class="idiff left right">'unpaired</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">unpairedBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"unpaired"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bam</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">unpairedBams</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="LC307" class="line" lang="scala"> <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">++=</span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">readsInRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">leftFlank</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="scala"> <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">++=</span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">readsInRegion</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rightFlank</span><span class="o" 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">@@ -324,14 +322,14 @@ class GapFiller(val region: GenomeRegion) {</td>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="scala"> <span class="nv" style="color: #008080;">assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">addReads</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="LC323" class="line" lang="scala"> <span class="nv" style="color: #008080;">assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">buildGraph</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">val</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">forward</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">reverse</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="nv" style="color: #008080;">assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">multiBridge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">right</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="nv" style="color: #008080;"><span class="idiff">loop</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">is</span>Empty</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;"><span class="idiff left">loop</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">non</span>Empty</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" loop: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">loop</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</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;">loop</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">patches</span> <span class="k" 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="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="LC329" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">f</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">forward</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;">reverse</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="LC330" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">patch</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">properOverlap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">,</span> <span class="nv" style="color: #008080;">GapFiller</span><span class="o" style="font-weight: 600;">.</span><span class="py">k</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// We should be very close in our closure estimation from alignments. Don't allow</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(<span class="idiff left">!</span></span><span class="nv" style="color: #008080;"><span class="idiff">patch</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><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 class="n" style="color: #333;">estimatedLength</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="nv" style="color: #008080;">patch</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="n" style="color: #333;">breakRadius</span><span class="o" style="font-weight: 600;">).</span><span class="py">abs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">estimatedLengthSlop</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="LC332" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;"><span class="idiff left">patch</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><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 class="n" style="color: #333;">estimatedLength</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="nv" style="color: #008080;">patch</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="n" style="color: #333;">breakRadius</span><span class="o" style="font-weight: 600;">).</span><span class="py">abs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">estimatedLengthSlop</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="LC333" class="line" lang="scala"> <span class="n" style="color: #333;">patches</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">patch</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="scala"> <span class="o" 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">@@ -340,7 +338,7 @@ class GapFiller(val region: GenomeRegion) {</td>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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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="nv" style="color: #008080;">lengths</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">patches</span><span class="o" style="font-weight: 600;">.</span><span class="py">map</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span><span class="o" style="font-weight: 600;">).</span><span class="py">toSet</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">verbose</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;"><span class="idiff left">patches</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">size</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">" patches; lengths "</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">lengths</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">s</span></span><span class="s" style="color: #d14;"><span class="idiff right">"{$patches.size} patches; lengths $lengths"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">lengths</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">estimatedLength</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="nv" style="color: #008080;">loop</span><span class="o" style="font-weight: 600;">.</span><span class="py">isEmpty</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">loop</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">estimatedLength</span><span class="o" style="font-weight: 600;">).</span><span class="py">abs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">estimatedLengthSlop</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="LC344" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">patch</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">patches</span><span class="o" style="font-weight: 600;">.</span><span class="py">head</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">@@ -358,11 +356,11 @@ class GapFiller(val region: GenomeRegion) {</td>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">breakRadius</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="LC358" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">minRadius</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">Assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">K</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">inserts</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;"><span class="idiff left right">'frags</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">bam</span> <span class="k" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">insertSizeMean</span> <span class="cm" style="color: #998; font-style: italic;">/*+ bam.insertSizeSigma*/</span><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="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">inserts</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"frags"</span></span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">{</span><span class="n" style="color: #333;">bam</span> <span class="k" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">insertSizeMean</span> <span class="cm" style="color: #998; font-style: italic;">/*+ bam.insertSizeSigma*/</span><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">insertMean</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">inserts</span><span class="o" style="font-weight: 600;">.</span><span class="py">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 class="nv" style="color: #008080;">inserts</span><span class="o" style="font-weight: 600;">.</span><span class="py">sum</span> <span class="o" style="font-weight: 600;">/</span> <span class="nv" style="color: #008080;">inserts</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span><span class="o" style="font-weight: 600;">).</span><span class="py">round</span><span class="o" style="font-weight: 600;">.</span><span class="py">toInt</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="LC361" 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="LC362" 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 class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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="LC365" 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="LC366" class="line" lang="scala"> <span class="nf" style="color: #900; 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -373,37 +371,37 @@ class GapFiller(val region: GenomeRegion) {</td>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="scala"> <span class="n" style="color: #333;">reads</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="scala"> <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>
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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="nf" style="color: #900; font-weight: 600;">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;">S<span class="idiff left right">ymbol</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="LC374" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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;">S<span class="idiff left right">tring</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="LC375" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="LC376" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//def recruitFrags(reg: Region) = mateMapOfType(reg, 'frags).values.toList</span></span>
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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="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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;"><span class="idiff left right">'frags</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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="s" style="color: #d14;"><span class="idiff left right">"frags"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="scala"></span>
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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="nf" style="color: #900; font-weight: 600;">recruitJumps</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>
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<pre style="margin: 0;"> <span id="LC382" 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="LC385" class="line" lang="scala"> <span class="nf" style="color: #900; 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="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;"><span class="idiff left right">'jumps</span></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="LC383" class="line" lang="scala"> <span class="nf" style="color: #900; 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="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"jumps"</span></span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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386
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="scala"> <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">++=</span> <span class="nv" style="color: #008080;">b</span><span class="o" style="font-weight: 600;">.</span><span class="py">recruitBadMates</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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387
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span><span class="idiff left right"> </span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span></span>
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389
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"# Recruiting jump bad mates: count="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">reads</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span><span class="o" style="font-weight: 600;">)</span></span>
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390
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="scala"> <span class="n" style="color: #333;">reads</span></span>
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391
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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392
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="scala"></span>
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393
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">longread</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">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;"><span class="idiff left right">'unpaired</span></span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="nc" style="color: #458; font-weight: 600;">Nil</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">longread</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">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="s" style="color: #d14;"><span class="idiff left right">"unpaired"</span></span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="nc" style="color: #458; font-weight: 600;">Nil</span></span>
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395
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="scala"></span>
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396
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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>
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397
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="scala"></span>
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398
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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>
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<td class="diff-line-num old old_line" data-linenumber="399" 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">
399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;"><span class="idiff left right">'unpaired</span></span><span class="o" style="font-weight: 600;">).</span><span class="py">filter</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">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>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"unpaired"</span></span><span class="o" style="font-weight: 600;">).</span><span class="py">filter</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">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>
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400
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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401
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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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<pre style="margin: 0;">+<span id="LC404" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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="k" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">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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<pre style="margin: 0;"> <span id="LC406" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">header</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;">SAMFileHeader</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="scala"> <span class="nv" style="color: #008080;">header</span><span class="o" style="font-weight: 600;">.</span><span class="py">addSequence</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;">SAMSequenceRecord</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">contig</span><span class="o" style="font-weight: 600;">.</span><span class="py">getName</span><span class="o" style="font-weight: 600;">,</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">contig</span><span class="o" style="font-weight: 600;">.</span><span class="py">getBases</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</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/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#41fa529971dd7270998497c479f938d56c59e3ea"><strong>src/main/scala/org/broadinstitute/pilon/GenomeFile.scala</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,43 +86,36 @@ class GenomeFile(val referenceFile: File, val targets : String = "") {</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="scala"> <span class="n" style="color: #333;">bamFiles</span> <span class="n" style="color: #333;">foreach</span> <span class="o" style="font-weight: 600;">{</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">validateSeqs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">contigsOfInterest</span><span class="o" style="font-weight: 600;">)}</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">strays</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">contains</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="ss" style="color: #990073;"><span class="idiff">'circles</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">strays</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">Circles</span></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="LC90" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Scanning BAMs"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// Scan BAMs in parallel</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//bamFiles.filter({_.bamType != 'unpaired}).par.map(_.scan(contigsOfInterest))</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="scala"> <span class="nv" style="color: #008080;">bamFiles</span><span class="o" style="font-weight: 600;">.</span><span class="py">par</span><span class="o" style="font-weight: 600;">.</span><span class="py">map</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">scan</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">contigsOfInterest</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="scala"> <span class="nv" style="color: #008080;">bamFiles</span><span class="o" style="font-weight: 600;">.</span><span class="py">map</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">scan</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">contigsOfInterest</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">circles</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Scaffold</span><span class="o" style="font-weight: 600;">.</span><span class="py">findHgapCircles</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>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// If assemble novel sequence up front, so that we can potentially place the</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// contigs into scaffolds when we process them.</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff right">'n</span>ovel</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">N</span>ovel</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="scala"> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">novelContigs</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">assembleNovel</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>
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102
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100
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<pre style="margin: 0;"> <span id="LC100" 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;">var</span> <span class="n" style="color: #333;">chunks</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">regions</span><span class="o" style="font-weight: 600;">.</span><span class="py">map</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span><span class="o" style="font-weight: 600;">).</span><span class="py">flatten</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">threads</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>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// Do parallel processing randomly to even out load if all the </span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// big chunks are early in the file</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="scala"> <span class="n" style="color: #333;">chunks</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Random</span><span class="o" style="font-weight: 600;">.</span><span class="py">shuffle</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chunks</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="scala"> <span class="nv" style="color: #008080;">chunks</span><span class="o" style="font-weight: 600;">.</span><span class="py">par</span> <span class="n" style="color: #333;">foreach</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>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="scala"> <span class="n" style="color: #333;">chunks</span> <span class="n" style="color: #333;">foreach</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>
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110
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Processing "</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>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="scala"> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">initializePileUps</span></span>
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112
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="scala"> <span class="n" style="color: #333;">bamFiles</span> <span class="n" style="color: #333;">foreach</span> <span class="o" style="font-weight: 600;">{</span> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">processBam</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="o" style="font-weight: 600;">}</span></span>
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113
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="scala"> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">postProcess</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff right">'c</span>ircles</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">C</span>ircles</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span></span>
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115
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="scala"> <span class="cm" style="color: #998; font-style: italic;">/*(r.contig.length < 5000 && r.contig.length >= 1000) ||*/</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">circles</span> <span class="n" style="color: #333;">contains</span> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">contig</span><span class="o" style="font-weight: 600;">.</span><span class="py">getName</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">verbose</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">r</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span> might be a circle!"</span><span class="o" style="font-weight: 600;">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">verbose</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">s</span></span><span class="s" style="color: #d14;"><span class="idiff right">"$r</span> might be a circle!"</span><span class="o" style="font-weight: 600;">)</span></span>
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117
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="scala"> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">closeCircle</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">circles</span><span class="o" style="font-weight: 600;">.</span><span class="py">getOrElse</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">contig</span><span class="o" style="font-weight: 600;">.</span><span class="py">getName</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">))</span></span>
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118
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">vcf</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">intersect</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></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="ss" style="color: #990073;"><span class="idiff">'snps</span></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">'indels</span></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">'gaps</span></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">'local</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)).</span></span><span class="py"><span class="idiff right">isEmpty</span></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="LC112" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">vcf</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;"><span class="idiff left">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixSnps</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixIndels</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixGaps</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">fixLocal</span></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="LC113" class="line" lang="scala"> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">identifyAndFixIssues</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// If we don't need pileups for VCF later, free up the memory now!</span></span>
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122
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">vcf</span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">finalizePileUps</span></span>
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123
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">r</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span> log:"</span><span class="o" style="font-weight: 600;">)</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="scala"> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">printLog</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">s</span></span><span class="s" style="color: #d14;"><span class="idiff right">"$r</span> log:"</span><span class="o" style="font-weight: 600;">)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="scala"> <span class="nv" style="color: #008080;">r</span><span class="o" style="font-weight: 600;">.</span><span class="py">printLog</span><span class="o" style="font-weight: 600;"><span class="idiff left right">()</span></span></span>
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126
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Finished processing "</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>
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127
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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128
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="scala"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,7 +124,7 @@ class GenomeFile(val referenceFile: File, val targets : String = "") {</td>
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131
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="scala"> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</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;">BufferedWriter</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;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">changesFile</span><span class="o" style="font-weight: 600;">)))</span></span>
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132
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="kc" style="font-weight: 600;">null</span></span>
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133
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fastaFile</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">outputFile</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">".fasta"</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="nv" style="color: #008080;">fastaWriter</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(<span class="idiff left">!</span></span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">isEmpty</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fastaWriter</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;"><span class="idiff left">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixSnps</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixIndels</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixGaps</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixLocal</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">fixNovel</span></span><span class="o" style="font-weight: 600;">)</span></span>
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135
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="scala"> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</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;">BufferedWriter</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;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fastaFile</span><span class="o" style="font-weight: 600;">)))</span></span>
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136
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="kc" style="font-weight: 600;">null</span></span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="scala"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -160,7 +153,7 @@ class GenomeFile(val referenceFile: File, val targets : String = "") {</td>
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160
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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161
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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162
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// Write the FASTA all at once rather than in chunks for formatting reasons</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(<span class="idiff left">!</span></span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">isEmpty</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">fastaWriter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">null</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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164
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing updated "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">newName</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" to "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">fastaFile</span><span class="o" style="font-weight: 600;">)</span></span>
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165
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixedRegions</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">reg</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">{</span> <span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">bases</span> <span class="o" style="font-weight: 600;">}</span></span>
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166
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">bases</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixedRegions</span> <span class="n" style="color: #333;">reduceLeft</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="k" style="font-weight: 600;">_</span><span class="o" style="font-weight: 600;">}</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">{</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,7 +161,7 @@ class GenomeFile(val referenceFile: File, val targets : String = "") {</td>
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168
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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169
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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170
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="scala"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff right">'n</span>ovel</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">N</span>ovel</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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172
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">novelContigs</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">novelContigs</span></span>
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173
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">n</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="nv" style="color: #008080;">novelContigs</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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174
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">header</span> <span class="k" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"pilon_novel_%03d"</span><span class="o" style="font-weight: 600;">.</span><span class="py">format</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;">1</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="176" style="width: 35px; color: rgba(0,0,0,0.3); 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="169" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -176,7 +169,7 @@ class GenomeFile(val referenceFile: File, val targets : String = "") {</td>
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176
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">writeFastaElement</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fastaWriter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">,</span> <span class="nf" style="color: #900; font-weight: 600;">novelContigs</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>
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177
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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178
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(<span class="idiff left">!</span></span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">isEmpty</span></span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;">fastaWriter</span><span class="o" style="font-weight: 600;">.</span><span class="py">close</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">fastaWriter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">null</span></span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;">fastaWriter</span><span class="o" style="font-weight: 600;">.</span><span class="py">close</span></span>
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180
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">vcf</span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;">vcf</span><span class="o" style="font-weight: 600;">.</span><span class="py">close</span></span>
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181
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">changes</span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;">changesWriter</span><span class="o" style="font-weight: 600;">.</span><span class="py">close</span></span>
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182
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">coverageSummary</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>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,7 +180,7 @@ class GenomeFile(val referenceFile: File, val targets : String = "") {</td>
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187
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">totalBaseCount</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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188
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">)</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">bamTypes</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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189
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">typeBaseCount</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">files</span><span class="o" style="font-weight: 600;">.</span><span class="py">map</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">baseCount</span><span class="o" style="font-weight: 600;">).</span><span class="py">sum</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Mean "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">t</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="py"><span class="idiff right">name</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" coverage: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">roundDiv</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">typeBaseCount</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">genomeSize</span><span class="o" style="font-weight: 600;">))</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Mean "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" coverage: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">roundDiv</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">typeBaseCount</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">genomeSize</span><span class="o" style="font-weight: 600;">))</span></span>
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191
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="scala"> <span class="n" style="color: #333;">totalBaseCount</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">typeBaseCount</span></span>
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192
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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193
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Mean total coverage: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">roundDiv</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">totalBaseCount</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">genomeSize</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="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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -204,16 +197,16 @@ class GenomeFile(val referenceFile: File, val targets : String = "") {</td>
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204
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">verbose</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">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="nv" style="color: #008080;">contig</span><span class="o" style="font-weight: 600;">.</span><span class="py">getName</span><span class="o" style="font-weight: 600;">)</span></span>
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205
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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206
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//genomeGraph.buildGraph</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">verbose</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">println</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">verbose</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;"><span class="idiff left right">()</span></span></span>
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208
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">assembler</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;">Assembler</span><span class="o" style="font-weight: 600;">()</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="scala"> <span class="n" style="color: #333;">bamFiles</span> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">{</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'jumps</span></span><span class="o" style="font-weight: 600;">}</span> <span class="n" style="color: #333;">foreach</span> <span class="o" style="font-weight: 600;">{</span> <span class="n" style="color: #333;">bam</span> <span class="k" style="font-weight: 600;">=></span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="scala"> <span class="n" style="color: #333;">bamFiles</span> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">{</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"jumps"</span></span><span class="o" style="font-weight: 600;">}</span> <span class="n" style="color: #333;">foreach</span> <span class="o" style="font-weight: 600;">{</span> <span class="n" style="color: #333;">bam</span> <span class="k" style="font-weight: 600;">=></span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">reads</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">getUnaligned</span></span>
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211
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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="nv" style="color: #008080;">reads</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" unmapped reads"</span><span class="o" style="font-weight: 600;">)</span></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="scala"> <span class="nv" style="color: #008080;">assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">addReads</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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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"...assembling contigs"</span><span class="o" style="font-weight: 600;">)</span></span>
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215
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">contigs</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">novel</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genomeGraph</span><span class="o" style="font-weight: 600;">)</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="scala"> <span class="n" style="color: #333;">println</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;"><span class="idiff left right">()</span></span></span>
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217
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">contigLengths</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contigs</span> <span class="n" style="color: #333;">map</span> <span class="o" style="font-weight: 600;">{</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span><span class="o" style="font-weight: 600;">}</span></span>
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218
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Assembled %d novel contigs containing %d bases"</span><span class="o" style="font-weight: 600;">.</span><span class="py">format</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">contigs</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span><span class="o" style="font-weight: 600;">,</span> <span class="nv" style="color: #008080;">contigLengths</span><span class="o" style="font-weight: 600;">.</span><span class="py">sum</span><span class="o" style="font-weight: 600;">))</span></span>
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="scala"> <span class="n" style="color: #333;">contigs</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); 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="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -244,7 +237,7 @@ class GenomeFile(val referenceFile: File, val targets : String = "") {</td>
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244
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="scala"></span>
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245
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parseTargetFile</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="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>
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246
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="scala"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="scala"> <span class="nv" style="color: #008080;">Source</span><span class="o" style="font-weight: 600;">.</span><span class="py">fromFile</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="py">getLines</span><span class="o" style="font-weight: 600;">.</span><span class="py">flatMap</span><span class="o" style="font-weight: 600;">({</span><span class="nf" style="color: #900; font-weight: 600;">parseTargetString</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="py">toList</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="scala"> <span class="nv" style="color: #008080;">Source</span><span class="o" style="font-weight: 600;">.</span><span class="py">fromFile</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="py">getLines</span><span class="o" style="font-weight: 600;"><span class="idiff left right">()</span>.</span><span class="py">flatMap</span><span class="o" style="font-weight: 600;">({</span><span class="nf" style="color: #900; font-weight: 600;">parseTargetString</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="py">toList</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ioe</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Exception</span> <span class="o" 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="LC243" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<li id="22c74dec22ce9a07c028f8ea0d3fa62179ca3f4f">
<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#22c74dec22ce9a07c028f8ea0d3fa62179ca3f4f"><strong>src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -63,25 +63,27 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="scala"></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;">logString</span> <span class="k" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// Hack alert...if we're running multithreaded, buffer our output for atomic</span></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;">// write when we're done. Otherwise, we would rather see output as it happens.</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">log</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="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>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">threads</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="LC70" class="line" lang="scala"> <span class="n" style="color: #333;">logString</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">print</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>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">print</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>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">logln</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="kt" style="color: #458; font-weight: 600;">String</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="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="LC71" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</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="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</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="LC79" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printLog</span><span class="o" style="font-weight: 600;">()</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; 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="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">threads</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">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="nf" style="color: #900; font-weight: 600;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">logString</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printLog</span><span class="o" style="font-weight: 600;">()</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">logString</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>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">changeMap</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Map</span><span class="o" style="font-weight: 600;">.</span><span class="py">empty</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Int</span>, <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">Symbol</span>, <span class="kt" style="color: #458; font-weight: 600;">PileUp</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>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">addChange</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="n" style="color: #333;">kind</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="n" style="color: #333;">pu</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">PileUp</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="LC84" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</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="ss" style="color: #990073;">'amb</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">ambiguous</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="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="LC77" class="line" lang="scala"> <span class="k" style="font-weight: 600;">object</span> <span class="nc" style="color: #458; font-weight: 600;">ChangeKind</span> <span class="k" style="font-weight: 600;">extends</span> <span class="nc" style="color: #458; font-weight: 600;">Enumeration</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;">type</span> <span class="kt" style="color: #458; font-weight: 600;">ChangeKind</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Value</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="nv" style="color: #008080;">SNP</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">INS</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">DEL</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">AMB</span> <span class="k" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Value</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="scala"> <span class="k" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ChangeKind._</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="scala"></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">changeMap</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Map</span><span class="o" style="font-weight: 600;">.</span><span class="py">empty</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">Int</span>, <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">ChangeKind</span>, <span class="kt" style="color: #458; font-weight: 600;">PileUp</span><span class="o" style="font-weight: 600;">)]</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="scala"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">addChange</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="n" style="color: #333;">kind</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">ChangeKind</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pu</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">PileUp</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="LC86" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</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="nc" style="color: #458; font-weight: 600;">AMB</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">ambiguous</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="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="LC87" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">changed</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="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="LC88" class="line" lang="scala"> <span class="n" style="color: #333;">changeMap</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="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>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="scala"> <span class="o" 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">@@ -134,13 +136,13 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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<pre style="margin: 0;"> <span id="LC136" 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="LC137" 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="LC138" 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="nf" style="color: #900; font-weight: 600;">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;">S<span class="idiff left right">ymbol</span></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="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="LC139" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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;">S<span class="idiff left right">tring</span></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="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="LC140" 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="nf" style="color: #900; font-weight: 600;">nanoporeBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;"><span class="idiff left">'unpaired</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">filter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">{</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">subType</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">'nanopore</span></span><span class="o" style="font-weight: 600;">}</span></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="nf" style="color: #900; font-weight: 600;">nanoporeBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><span class="idiff left">"unpaired"</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">filter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">{</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">subType</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">"nanopore"</span></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="LC141" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pacbioBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;"><span class="idiff left">'unpaired</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">filter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">{</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">subType</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">'pacbio</span></span> <span class="o" style="font-weight: 600;">}</span></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="nf" style="color: #900; font-weight: 600;">pacbioBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><span class="idiff left">"unpaired"</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">filter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">{</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">subType</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">"pacbio"</span></span> <span class="o" style="font-weight: 600;">}</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="LC143" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fragBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="ss" style="color: #990073;"><span class="idiff left right">'frags</span></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fragBams</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bamsOfType</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"frags"</span></span><span class="o" style="font-weight: 600;">)</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="nf" style="color: #900; font-weight: 600;">longReadOnly</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">longread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">fragBams</span><span class="o" style="font-weight: 600;">.</span><span class="py">isEmpty</span></span>
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<pre style="margin: 0;"> <span id="LC148" 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">@@ -230,7 +232,7 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//meanReadLength = pileUpRegion.meanReadLength</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="scala"></span>
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// Pass 1: pull out values from pileups & call base changes</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixamb</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">iupac</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;"><span class="idiff left">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixList</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff">'amb</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixamb</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">iupac</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;"><span class="idiff left">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">fixAmb</span></span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="scala"> <span class="nf" style="color: #900; 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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236
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">pu</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">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>
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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">@@ -253,9 +255,9 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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253
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="scala"> <span class="nf" style="color: #900; 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="n" style="color: #333;">minDepth</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="sc" style="color: #d14;">'N'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nf" style="color: #900; font-weight: 600;">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="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">called</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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254
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="scala"> <span class="nf" style="color: #900; 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;">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="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">highConfidence</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">indel</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">confirmed</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="kc" style="font-weight: 600;">true</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">isInsertion</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">homoIndel</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">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;"><span class="idiff left right">'ins</span></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>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">isInsertion</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">homoIndel</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">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="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">INS</span></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>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">isDeletion</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">homoIndel</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="LC258" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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;"><span class="idiff left right">'del</span></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>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">DEL</span></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>
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259
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span> <span class="k" style="font-weight: 600;"><-</span> <span class="mi" style="color: #099;">1</span> <span class="n" style="color: #333;">until</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">deletion</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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260
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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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261
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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="py">deletions</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: #008080;">pu</span><span class="o" style="font-weight: 600;">.</span><span class="py">deletions</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -263,8 +265,8 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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263
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; 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="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">score</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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264
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266
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<pre style="margin: 0;"> <span id="LC266" 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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265
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267
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<pre style="margin: 0;"> <span id="LC267" 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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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="scala"> <span class="nf" style="color: #900; 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="nf" style="color: #900; font-weight: 600;">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;"><span class="idiff left right">'snp</span></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>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixamb</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">altBase</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="nf" style="color: #900; font-weight: 600;">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;"><span class="idiff left right">'amb</span></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>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="scala"> <span class="nf" style="color: #900; 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="nf" style="color: #900; font-weight: 600;">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="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">SNP</span></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>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixamb</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">altBase</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="nf" style="color: #900; font-weight: 600;">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="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">AMB</span></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>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="scala"> <span class="o" 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">@@ -283,15 +285,15 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">processBam</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bam</span><span class="k" 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="LC286" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="py"><span class="idiff right">name</span></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="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamFile</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>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</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="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamFile</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>
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287
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// This is a real kludge...</span></span>
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288
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">covBefore</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;">Int</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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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'jumps</span></span><span class="o" style="font-weight: 600;">)</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"jumps"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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290
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="scala"> <span class="nf" style="color: #900; 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>
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291
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">covBefore</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="nv" style="color: #008080;">pileUpRegion</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="py">depth</span><span class="o" style="font-weight: 600;">.</span><span class="py">toInt</span></span>
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292
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294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">coverage</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">process</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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293
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">logln</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"coverage "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">coverage</span><span class="o" style="font-weight: 600;">.</span><span class="py">toString</span><span class="o" style="font-weight: 600;">)</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'jumps</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"jumps"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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295
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="scala"> <span class="nf" style="color: #900; 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>
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296
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">fragCoverage</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="nv" style="color: #008080;">pileUpRegion</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="py">depth</span><span class="o" style="font-weight: 600;">.</span><span class="py">toInt</span> <span class="o" style="font-weight: 600;">-</span> <span class="nf" style="color: #900; font-weight: 600;">covBefore</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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297
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="scala"> <span class="n" style="color: #333;">bams</span> <span class="o" style="font-weight: 600;">::=</span> <span class="n" style="color: #333;">bam</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); 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="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -307,8 +309,8 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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307
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">logln</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"# IdentifyIssues: "</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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308
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="scala"> <span class="n" style="color: #333;">identifyIssueRegions</span></span>
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309
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixSnps</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff right">'s</span>nps</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixIndels</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff right">'i</span>ndels</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixSnps</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">S</span>nps</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixIndels</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">I</span>ndels</span></span>
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">snps</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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313
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">ins</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">dels</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</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">@@ -323,10 +325,10 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">cBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">base</span></span>
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324
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="nf" style="color: #900; font-weight: 600;">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>
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327
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<pre style="margin: 0;"> <span id="LC327" 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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326
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<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;"><span class="idiff left right">'snp</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">SNP</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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327
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="scala"> <span class="nf" style="color: #900; 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="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="py">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="nv" style="color: #008080;">cBase</span><span class="o" style="font-weight: 600;">.</span><span class="py">toString</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC330" 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="LC329" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'amb</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">AMB</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="scala"> <span class="nf" style="color: #900; 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="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">longread</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="LC333" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">iupac</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="LC334" 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>
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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">@@ -337,12 +339,12 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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337
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC340" 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>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<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;"><span class="idiff left right">'ins</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">INS</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">insert</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">insertion</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="scala"> <span class="nf" style="color: #900; 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>
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<pre style="margin: 0;"> <span id="LC345" 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>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="scala"> <span class="n" style="color: #333;">insBases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: #008080;">insert</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span></span>
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<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;"><span class="idiff left right">'del</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">DEL</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">deletion</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">deletion</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="scala"> <span class="nf" style="color: #900; 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>
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<pre style="margin: 0;"> <span id="LC350" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); 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="359" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -357,15 +359,15 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">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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358
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">logln</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Confirmed "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nConfirmed</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" of "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nonN</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="LC361" class="line" lang="scala"> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nConfirmed</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nonN</span><span class="o" style="font-weight: 600;">).</span><span class="py">formatted</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"%.2f"</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>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff right">'s</span>nps</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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="LC361" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">diploid</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">snps</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">amb</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span> snps"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">S</span>nps</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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="LC363" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">diploid</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">s</span></span><span class="s" style="color: #d14;"><span class="idiff right">"${snps+amb}</span> snps"</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;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s<span class="idiff left">nps</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> snps; "</span><span class="o" style="font-weight: 600;">)</span></span>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">amb</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> ambiguous bases"</span><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 class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="s" style="color: #d14;"><span class="idiff left right">"$snps</span> snps; "</span><span class="o" style="font-weight: 600;">)</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">s</span></span><span class="s" style="color: #d14;"><span class="idiff right">"$amb</span> ambiguous bases"</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff right">'i</span>ndels</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">ins</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">" small insertions totaling "</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">insBases</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> 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="nf" style="color: #900; font-weight: 600;">logln</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;"><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">dels</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">" small deletions totaling "</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">delBases</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> 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="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">I</span>ndels</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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="LC369" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">s</span></span><span class="s" style="color: #d14;"><span class="idiff right">"$ins small insertions totaling $insBases</span> bases"</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="nf" style="color: #900; font-weight: 600;">logln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">s</span></span><span class="s" style="color: #d14;"><span class="idiff right">", $dels small deletions totaling $delBases</span> bases"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC372" 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="LC373" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">duplications</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">duplicationEvents</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">@@ -378,7 +380,7 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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378
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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379
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="scala"></span>
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380
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// Try to fill gaps</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(<span class="idiff left">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixList</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff">'gaps</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">gaps</span><span class="o" style="font-weight: 600;">.</span><span class="py">nonEmpty</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;"><span class="idiff left">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">fixGaps</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">gaps</span><span class="o" style="font-weight: 600;">.</span><span class="py">nonEmpty</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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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="scala"> <span class="nf" style="color: #900; 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>
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384
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -392,7 +394,7 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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392
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="scala"></span>
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395
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<pre style="margin: 0;"> <span id="LC395" 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>
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">breaks</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">possibleBreaks</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(<span class="idiff left">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">fixList</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff">'local</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">breaks</span><span class="o" style="font-weight: 600;">.</span><span class="py">nonEmpty</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;"><span class="idiff left">Pilon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff right">fixLocal</span></span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">breaks</span><span class="o" style="font-weight: 600;">.</span><span class="py">nonEmpty</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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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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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397
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="scala"> <span class="nf" style="color: #900; 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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398
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">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 new_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -520,21 +522,21 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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520
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522
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">rBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">refBase</span><span class="o" style="font-weight: 600;">(</span><span class="nf" style="color: #900; font-weight: 600;">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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521
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523
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">cBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">pu</span><span class="o" style="font-weight: 600;">.</span><span class="py">baseCall</span><span class="o" style="font-weight: 600;">.</span><span class="py">base</span></span>
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<pre style="margin: 0;"> <span id="LC524" 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="LC523" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'snp</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">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 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="nv" style="color: #008080;"><span class="idiff">kind</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><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">"</span> "</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="s" style="color: #d14;">" "</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>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">SNP</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">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 class="idiff left right">snp</span> "</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="s" style="color: #d14;">" "</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>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">log</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;">pu</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">endLine</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'ins</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">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 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="nv" style="color: #008080;"><span class="idiff">kind</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><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">"</span> "</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"."</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">pu</span><span class="o" style="font-weight: 600;">.</span><span class="py">baseCall</span><span class="o" style="font-weight: 600;">.</span><span class="py">insertion</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">INS</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">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 class="idiff left right">ins</span> "</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"."</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">pu</span><span class="o" style="font-weight: 600;">.</span><span class="py">baseCall</span><span class="o" style="font-weight: 600;">.</span><span class="py">insertion</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">log</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;">pu</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">endLine</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'del</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">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 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="nv" style="color: #008080;"><span class="idiff">kind</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><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">"</span> "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">pu</span><span class="o" style="font-weight: 600;">.</span><span class="py">baseCall</span><span class="o" style="font-weight: 600;">.</span><span class="py">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 class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">DEL</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">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 class="idiff left right">del</span> "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">pu</span><span class="o" style="font-weight: 600;">.</span><span class="py">baseCall</span><span class="o" style="font-weight: 600;">.</span><span class="py">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 class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">log</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;">pu</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">endLine</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'amb</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">AMB</span></span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">verbose</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;">cBase</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="LC537" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">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 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="nv" style="color: #008080;"><span class="idiff">kind</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><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">"</span> "</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="s" style="color: #d14;">" "</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>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nf" style="color: #900; font-weight: 600;">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 class="idiff left right">amb</span> "</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="s" style="color: #d14;">" "</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>
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">debug</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">log</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;">pu</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">log</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">endLine</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="scala"> <span class="o" 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">@@ -640,7 +642,7 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)</td>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeChanges</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">changes</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">PrintWriter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newName</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;">name</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="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="LC645" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeChanges</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">changes</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">PrintWriter</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newName</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;">name</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixes</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">fixFixList</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="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>
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647
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">delta</span> <span class="k" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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646
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648
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fix</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">fixes</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#9301f94a8a30273eb398963b538f6f77373c915f"><strong>src/main/scala/org/broadinstitute/pilon/PileUp.scala</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="172" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -172,7 +172,7 @@ class PileUp {</td>
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172
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nv" style="color: #008080;">base</span><span class="o" style="font-weight: 600;">.</span><span class="py">toString</span> <span class="c1" style="color: #998; font-style: italic;">//+ (if (!homo) "/" + altBase else "")</span></span>
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173
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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174
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="scala"></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">baseMatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refBase</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Char</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">baseMatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refBase</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">Char</span><span class="o" style="font-weight: 600;">)</span> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">{</span><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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176
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="scala"> <span class="n" style="color: #333;">refBase</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">base</span> <span class="c1" style="color: #998; font-style: italic;">// TODO: handle IUPAC codes</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="scala"></span>
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<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#3fe73caca959968d50ca8052b982e85ac7cf08f2"><strong>src/main/scala/org/broadinstitute/pilon/PileUpRegion.scala</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@</td>
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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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<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.<span class="idiff left right">collection.Java</span>Converters._</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;">scala.<span class="idiff left right">jdk.Collection</span>Converters._</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;">htsjdk.samtools._</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;">Utils._</span></span>
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<pre style="margin: 0;"> <span id="LC25" 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">@@ -220,7 +220,7 @@ class PileUpRegion(name: String, start: Int, stop: Int)</td>
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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="LC222" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; 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="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">locus</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">": "</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">pileups</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="scala"> <span class="nf" style="color: #900; 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="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">s</span></span><span class="s" style="color: #d14;"><span class="idiff right">"${locus(i)}: ${pileups(i)}"</span></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>
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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="nf" style="color: #900; font-weight: 600;">postProcess</span> <span class="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>
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<li id="b5368e22ab004e3abd523db7a2c70531cd4f1c46">
<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#b5368e22ab004e3abd523db7a2c70531cd4f1c46"><strong>src/main/scala/org/broadinstitute/pilon/Pilon.scala</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,9 +22,18 @@ package org.broadinstitute.pilon</td>
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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;">java.io.File</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="scala"></span>
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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;">Pilon</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// types of fixing we know about</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixChoices</span> <span class="k" 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="ss" style="color: #990073;">'snps</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'indels</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'gaps</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'local</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">experimentalFixChoices</span> <span class="k" 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="ss" style="color: #990073;">'amb</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'breaks</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'circles</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'novel</span><span class="o" style="font-weight: 600;">,</span> <span class="ss" style="color: #990073;">'scaffolds</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixChoices</span><span class="k" 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="s" style="color: #d14;">"snps"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"indels"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"gaps"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"local"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">experimentalFixChoices</span> <span class="k" 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="s" style="color: #d14;">"amb"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"breaks"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"circles"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"novel"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"scaffolds"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="scala"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fixSnps</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="LC29" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fixIndels</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="LC30" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fixGaps</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="LC31" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fixLocal</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="LC32" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fixAmb</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fixBreaks</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="LC34" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fixCircles</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fixNovel</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">fixScaffolds</span> <span class="k" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span></span>
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28
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// input parameters</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">bamFiles</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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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,7 +70,6 @@ object Pilon {</td>
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<pre style="margin: 0;"> <span id="LC70" 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="LC71" 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="LC72" 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="LC73" 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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66
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// Global computed data</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">@@ -70,7 +78,7 @@ object Pilon {</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// for logging to output files</span></span>
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71
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<pre style="margin: 0;"> <span id="LC79" 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>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="scala"></span>
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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="nf" style="color: #900; font-weight: 600;">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>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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="k" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC82" 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>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Version</span><span class="o" style="font-weight: 600;">.</span><span class="py">version</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">optionParse</span><span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">.</span><span class="py">toList</span><span class="o" 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">@@ -84,11 +92,9 @@ object Pilon {</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">setDefaultParallelism</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC95" 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>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// if we're doing local reassembly</span></span>
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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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">fixList</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff">'gaps</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fixList</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff">'local</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fixList</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff">'scaffolds</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="scala"> <span class="n" style="color: #333;">strays</span> <span class="o" style="font-weight: 600;">&=</span> <span class="n" style="color: #333;"><span class="idiff left">fixGaps</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">fixLocal</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">fixScaffolds</span></span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bamFiles</span><span class="o" style="font-weight: 600;">.</span><span class="py">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>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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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">@@ -101,7 +107,7 @@ object Pilon {</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Genome: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomePath</span><span class="o" style="font-weight: 600;">)</span></span>
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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="nv" style="color: #008080;">genome</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;">GenomeFile</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;">genomePath</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">targets</span><span class="o" style="font-weight: 600;">)</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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;">m<span class="idiff left">ap</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">{</span></span><span class="nv" style="color: #008080;"><span class="idiff">_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">name</span></span><span class="o" style="font-weight: 600;"><span class="idiff">}</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff right">m</span>kString</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>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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="nf" style="color: #900; font-weight: 600;">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>
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105
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="scala"> <span class="nv" style="color: #008080;">genome</span><span class="o" style="font-weight: 600;">.</span><span class="py">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>
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106
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="scala"> <span class="nf" style="color: #900; 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>
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<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">@@ -111,9 +117,8 @@ object Pilon {</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</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="LC114" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">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>
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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="nf" style="color: #900; font-weight: 600;">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="idiff left right"> </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="LC121" class="line" lang="scala"> <span class="n" style="color: #333;">list</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="LC116" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;">Nil</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="LC122" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--help"</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>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">help</span><span class="o" 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">@@ -123,7 +128,7 @@ object Pilon {</td>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// println(Version.version)</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="scala"> <span class="nv" style="color: #008080;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="py">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>
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125
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--bam"</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>
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126
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<pre style="margin: 0;">-<span id="LC126" 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;"><span class="idiff left right">'bam</span></span><span class="o" style="font-weight: 600;">)</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" 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="s" style="color: #d14;"><span class="idiff left right">"bam"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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127
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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128
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--changes"</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>
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129
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="scala"> <span class="n" style="color: #333;">changes</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 unfold js-unfold old_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="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,7 +162,7 @@ object Pilon {</td>
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157
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="scala"> <span class="n" style="color: #333;">flank</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">value</span><span class="o" style="font-weight: 600;">.</span><span class="py">toInt</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--frags"</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>
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<pre style="margin: 0;">-<span id="LC160" 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;"><span class="idiff left right">'frags</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC165" 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="s" style="color: #d14;"><span class="idiff left right">"frags"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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161
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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162
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--gapmargin"</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>
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163
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="scala"> <span class="n" style="color: #333;">gapMargin</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">value</span><span class="o" style="font-weight: 600;">.</span><span class="py">toInt</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,7 +171,7 @@ object Pilon {</td>
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166
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="scala"> <span class="n" style="color: #333;">genomePath</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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167
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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168
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--jumps"</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>
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169
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<pre style="margin: 0;">-<span id="LC169" 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;"><span class="idiff left right">'jumps</span></span><span class="o" style="font-weight: 600;">)</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" 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="s" style="color: #d14;"><span class="idiff left right">"jumps"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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170
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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171
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--K"</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>
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172
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="scala"> <span class="nv" style="color: #008080;">Assembler</span><span class="o" style="font-weight: 600;">.</span><span class="py">K</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">value</span><span class="o" style="font-weight: 600;">.</span><span class="py">toInt</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,7 +192,7 @@ object Pilon {</td>
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187
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192
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<pre style="margin: 0;"> <span id="LC192" 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>
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188
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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189
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194
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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;">"--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>
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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;"><span class="idiff left">'unpaired</span></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">'nanopore</span></span><span class="o" style="font-weight: 600;">)</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" 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="s" style="color: #d14;"><span class="idiff left">"unpaired"</span></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">"nanopore"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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191
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<pre style="margin: 0;"> <span id="LC196" 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>
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192
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197
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<pre style="margin: 0;"> <span id="LC197" 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>
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193
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -204,7 +209,7 @@ object Pilon {</td>
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204
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209
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<pre style="margin: 0;"> <span id="LC209" 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>
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205
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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206
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211
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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;">"--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>
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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;"><span class="idiff left">'unpaired</span></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">'pacbio</span></span><span class="o" style="font-weight: 600;">)</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" 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="s" style="color: #d14;"><span class="idiff left">"unpaired"</span></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">"pacbio"</span></span><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 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>
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209
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<pre style="margin: 0;"> <span id="LC214" 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>
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210
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -212,7 +217,8 @@ object Pilon {</td>
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212
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217
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<pre style="margin: 0;"> <span id="LC217" 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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213
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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214
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--threads"</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>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="scala"> <span class="n" style="color: #333;">threads</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">value</span><span class="o" style="font-weight: 600;">.</span><span class="py">toInt</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"--threads argument no longer supported; ignoring!"</span><span class="o" style="font-weight: 600;">)</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//threads = value.toInt</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--tracks"</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>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="scala"> <span class="n" style="color: #333;">tracks</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 unfold js-unfold old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -221,12 +227,12 @@ object Pilon {</td>
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221
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// trSafe = true</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// optionParse(tail)</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--unpaired"</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>
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<pre style="margin: 0;">-<span id="LC224" 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;"><span class="idiff left right">'unpaired</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC230" 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="s" style="color: #d14;"><span class="idiff left right">"unpaired"</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--variant"</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>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// variant calling mode</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="scala"> <span class="n" style="color: #333;">vcf</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="LC229" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">+=</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'breaks</span></span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"breaks"</span></span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">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>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//multiClosure = true</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="s" style="color: #d14;">"--vcf"</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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -244,10 +250,21 @@ object Pilon {</td>
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">option</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>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Unknown option "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">option</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="scala"> <span class="nv" style="color: #008080;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="py">exit</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="LC253" class="line" lang="scala"> <span class="k" style="font-weight: 600;">case</span> <span class="nc" style="color: #458; font-weight: 600;">Nil</span> <span class="k" style="font-weight: 600;">=></span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="scala"> <span class="n" style="color: #333;">fixSnps</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="s" style="color: #d14;">"snps"</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="scala"> <span class="n" style="color: #333;">fixIndels</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="s" style="color: #d14;">"indels"</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="scala"> <span class="n" style="color: #333;">fixGaps</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="s" style="color: #d14;">"gaps"</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="scala"> <span class="n" style="color: #333;">fixLocal</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="s" style="color: #d14;">"local"</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="scala"> <span class="n" style="color: #333;">fixAmb</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="s" style="color: #d14;">"amb"</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="scala"> <span class="n" style="color: #333;">fixBreaks</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="s" style="color: #d14;">"breaks"</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="scala"> <span class="n" style="color: #333;">fixCircles</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="s" style="color: #d14;">"circles"</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="scala"> <span class="n" style="color: #333;">fixNovel</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="s" style="color: #d14;">"novel"</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="scala"> <span class="n" style="color: #333;">fixScaffolds</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fixList</span> <span class="n" style="color: #333;">contains</span> <span class="s" style="color: #d14;">"scaffolds"</span></span>
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248
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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249
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="scala"> </span>
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250
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parseFixList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fix</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="k" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">{</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// types of fixing we know about</span></span>
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251
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fixes</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">fix</span><span class="o" style="font-weight: 600;">.</span><span class="py">split</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>
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252
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nf" style="color: #900; font-weight: 600;">fix</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="sc" style="color: #d14;">'+'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nf" style="color: #900; font-weight: 600;">fix</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="sc" style="color: #d14;">'-'</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">fixList</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Set</span><span class="o" style="font-weight: 600;">.</span><span class="py">empty</span></span>
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253
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">f</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">fixes</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="255" style="width: 35px; color: rgba(0,0,0,0.3); 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="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -255,7 +272,7 @@ object Pilon {</td>
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255
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"none"</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">fixList</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">Set</span><span class="o" style="font-weight: 600;">.</span><span class="py">empty</span></span>
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256
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273
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<pre style="margin: 0;"> <span id="LC273" 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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257
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">plusMinus</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nf" style="color: #900; font-weight: 600;">f</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="sc" style="color: #d14;">'-'</span><span class="o" style="font-weight: 600;">)</span> <span class="nf" style="color: #900; font-weight: 600;">f</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="k" style="font-weight: 600;">else</span> <span class="sc" style="color: #d14;">'+'</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fsym</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nf" style="color: #900; font-weight: 600;">f</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;">plusMinus</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">Symbol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">substring</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">))</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="nc" style="color: #458; font-weight: 600;"><span class="idiff">Symbol</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span></span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">fsym</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nf" style="color: #900; font-weight: 600;">f</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;">plusMinus</span><span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: #008080;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="py"><span class="idiff">substring</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</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">f</span></span></span>
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259
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fixChoices</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">fsym</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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260
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">plusMinus</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'+'</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fsym</span></span>
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<td class="diff-line-num old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
261
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">fsym</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -264,14 +281,14 @@ object Pilon {</td>
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264
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Warning: experimental fix option "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">)</span></span>
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265
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">plusMinus</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'+'</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fsym</span></span>
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266
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="scala"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">fsym</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fsym</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'bases</span></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="LC284" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fsym</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">"bases"</span></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="LC285" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">// for backward compatibility, 'bases applies to both 'snps and 'indels</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">plusMinus</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'+'</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">+=</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'snps</span></span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">+=</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'indels</span></span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"snps"</span></span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"indels"</span></span></span>
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<pre style="margin: 0;"> <span id="LC289" 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>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">-=</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'snps</span></span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">-=</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'indels</span></span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">-=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"snps"</span></span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="scala"> <span class="n" style="color: #333;">fixList</span> <span class="o" style="font-weight: 600;">-=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"indels"</span></span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC293" 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>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Error: unknown fix option "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">)</span></span>
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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">@@ -286,21 +303,8 @@ object Pilon {</td>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">filePath</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">outdir</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;">fileName</span> <span class="k" style="font-weight: 600;">else</span> <span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">outdir</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;">fileName</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="scala"> <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;">filePath</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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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="nf" style="color: #900; font-weight: 600;">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="LC292" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">parPkgObj</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">scala</span><span class="o" style="font-weight: 600;">.</span><span class="py">collection</span><span class="o" style="font-weight: 600;">.</span><span class="py">parallel</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">`package`</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">defaultTaskSupportField</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">parPkgObj</span><span class="o" style="font-weight: 600;">.</span><span class="py">getClass</span><span class="o" style="font-weight: 600;">.</span><span class="py">getDeclaredFields</span><span class="o" style="font-weight: 600;">.</span><span class="py">find</span><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="scala"> <span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">getName</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"defaultTaskSupport"</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}.</span><span class="py">get</span></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="scala"> <span class="nv" style="color: #008080;">defaultTaskSupportField</span><span class="o" style="font-weight: 600;">.</span><span class="py">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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<pre style="margin: 0;">-<span id="LC298" class="line" lang="scala"> <span class="nv" style="color: #008080;">defaultTaskSupportField</span><span class="o" style="font-weight: 600;">.</span><span class="py">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="n" style="color: #333;">parPkgObj</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="scala"> <span class="k" style="font-weight: 600;">new</span> <span class="nv" style="color: #008080;">scala</span><span class="o" style="font-weight: 600;">.</span><span class="py">collection</span><span class="o" style="font-weight: 600;">.</span><span class="py">parallel</span><span class="o" style="font-weight: 600;">.</span><span class="py">ForkJoinTaskSupport</span><span class="o" style="font-weight: 600;">(</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="scala"> <span class="k" style="font-weight: 600;">new</span> <span class="nv" style="color: #008080;">scala</span><span class="o" style="font-weight: 600;">.</span><span class="py">concurrent</span><span class="o" style="font-weight: 600;">.</span><span class="py">forkjoin</span><span class="o" style="font-weight: 600;">.</span><span class="py">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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<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>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">usage</span> <span class="k" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="scala"><span class="s" style="color: #d14;"> Usage: pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam]</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="scala"><span class="s" style="color: #d14;"> [...other options...]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -324,6 +328,10 @@ object Pilon {</td>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="scala"><span class="s" style="color: #d14;"> --bam any.bam</span></span>
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="scala"><span class="s" style="color: #d14;"> A bam file of unknown type; Pilon will scan it and attempt to classify it as one</span></span>
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="scala"><span class="s" style="color: #d14;"> of the above bam types.</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="scala"><span class="s" style="color: #d14;"> --nanopore ont.bam</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="scala"><span class="s" style="color: #d14;"> A bam file containing Oxford Nanopore read alignments. Experimental.</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="scala"><span class="s" style="color: #d14;"> --pacbio pb.bam</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="scala"><span class="s" style="color: #d14;"> A bam file containing Pacific Biosciences read alignments. Experimental.</span></span>
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327
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="scala"><span class="s" style="color: #d14;"> OUTPUTS:</span></span>
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328
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="scala"><span class="s" style="color: #d14;"> --output prefix</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="scala"><span class="s" style="color: #d14;"> Prefix for output files</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -377,8 +385,6 @@ object Pilon {</td>
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377
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="scala"><span class="s" style="color: #d14;"> scaffold00001 and coordinates 10000-20000 of scaffold00002.</span></span>
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378
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="scala"><span class="s" style="color: #d14;"> If "targetlist" is the name of a file, each line will be treated as a target</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="scala"><span class="s" style="color: #d14;"> specification.</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="scala"><span class="s" style="color: #d14;"> --threads</span></span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="scala"><span class="s" style="color: #d14;"> Degree of parallelism to use for certain processing (default 1). Experimental.</span></span>
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382
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="scala"><span class="s" style="color: #d14;"> --verbose</span></span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="scala"><span class="s" style="color: #d14;"> More verbose output.</span></span>
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384
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="scala"><span class="s" style="color: #d14;"> --debug</span></span>
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<li id="5d7fca8bf098e437cfd1a54fa348e3b22c998c41">
<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#5d7fca8bf098e437cfd1a54fa348e3b22c998c41"><strong>src/main/scala/org/broadinstitute/pilon/Scaffold.scala</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,7 +28,7 @@ package org.broadinstitute.pilon</td>
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28
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28
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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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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="scala"></span>
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31
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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.<span class="idiff left right">collection.Java</span>Converters._</span></span>
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31
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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.<span class="idiff left right">jdk.Collection</span>Converters._</span></span>
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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>
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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>
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<pre style="margin: 0;"> <span id="LC34" 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">@@ -221,7 +221,7 @@ object Scaffold {</td>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="scala"> <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>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">analyzeStrays</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bam</span><span class="k" 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="LC224" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">mm</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">strayMateMap</span><span class="o" style="font-weight: 600;">.</span><span class="py">pairs</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">mm</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">strayMateMap</span><span class="o" style="font-weight: 600;">.</span><span class="py">pairs</span><span class="o" style="font-weight: 600;"><span class="idiff left right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">sigma</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">insertSizeSigma</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">scaffolds</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">bam</span><span class="o" style="font-weight: 600;">.</span><span class="py">getSeqs</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">scaffoldSizes</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">scaffolds</span><span class="o" style="font-weight: 600;">.</span><span class="py">map</span><span class="o" style="font-weight: 600;">({</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">getSequenceLength</span><span class="o" 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">@@ -269,16 +269,16 @@ object Scaffold {</td>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="scala"></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">analyze</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamFiles</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">analyze</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamFiles</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 class="idiff left">=</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">{</span></span>
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Analyze scaffolds"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bam</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">bamFiles</span> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">{</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'jumps</span></span><span class="o" style="font-weight: 600;">})</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bam</span> <span class="k" style="font-weight: 600;"><-</span> <span class="n" style="color: #333;">bamFiles</span> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">{</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">"jumps"</span></span><span class="o" style="font-weight: 600;">})</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">analyzeStrays</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="scala"></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">findHgapCircles</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bamFiles</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="kt" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">String</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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<pre style="margin: 0;">-<span id="LC280" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left">List</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">contains</span></span><span class="idiff"> </span><span class="ss" style="color: #990073;"><span class="idiff right">'c</span>ircles</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="LC281" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">endAlignments</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamFiles</span> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">{</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">==</span> <span class="ss" style="color: #990073;"><span class="idiff left right">'unpaired</span></span><span class="o" style="font-weight: 600;">}</span> <span class="n" style="color: #333;">flatMap</span> <span class="n" style="color: #333;">findEndAlignments</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">Pilon</span><span class="o" style="font-weight: 600;">.</span><span class="py">fix<span class="idiff left right">C</span>ircles</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="LC281" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">endAlignments</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamFiles</span> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">{</span><span class="nv" style="color: #008080;">_</span><span class="o" style="font-weight: 600;">.</span><span class="py">bamType</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">"unpaired"</span></span><span class="o" style="font-weight: 600;">}</span> <span class="n" style="color: #333;">flatMap</span> <span class="n" style="color: #333;">findEndAlignments</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">findCircles</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">endAlignments</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC283" 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;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span></span>
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<li id="eb01396af0fb64925f2389164b4ca0c257ae7f11">
<a href="https://salsa.debian.org/med-team/pilon/-/compare/b51bae118d0a257eb81cf8b4b4da817a9e1e21f1...4b8359ec03af8333fa579fef248e56dea2f035e7#eb01396af0fb64925f2389164b4ca0c257ae7f11"><strong>src/main/scala/org/broadinstitute/pilon/Vcf.scala</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,7 +90,7 @@ class Vcf(val file: File, val contigsWithSizes: List[(String, Int)] = Nil) {</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">p</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">pileUp</span><span class="o" style="font-weight: 600;">.</span><span class="py">delPct</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//(rBase + bcString, rBase.toString, "1/1", depth - pileUp.deletions, pileUp.deletions)</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//(rBase + bcString, rBase.toString, callType, pileUp.mqSum - pileUp.delQual, pileUp.delQual)</span></span>
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<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;">rBase</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bcString</span><span class="o" style="font-weight: 600;">,</span> <span class="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="py">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">callType</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="scala"> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="py"><span class="idiff right">toString</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bcString</span><span class="o" style="font-weight: 600;">,</span> <span class="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="py">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">callType</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="scala"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indelOk</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">embedded</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">isInsertion</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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95
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="scala"> <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>
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96
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96
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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="nv" style="color: #008080;">rBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">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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<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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,7 +98,7 @@ class Vcf(val file: File, val contigsWithSizes: List[(String, Int)] = Nil) {</td>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">p</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">pileUp</span><span class="o" style="font-weight: 600;">.</span><span class="py">insPct</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//(rBase.toString, rBase + bcString, "1/1", depth - pileUp.insertions, pileUp.insertions)</span></span>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="scala"> <span class="c1" style="color: #998; font-style: italic;">//(rBase.toString, rBase + bcString, callType, pileUp.mqSum - pileUp.insQual, pileUp.insQual)</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="scala"> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="py">toString</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;">bcString</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">callType</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="scala"> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;">.</span><span class="py">toString</span><span class="o" style="font-weight: 600;">,</span> <span class="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="py"><span class="idiff right">toString</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bcString</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">callType</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">)</span></span>
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102
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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="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">homo</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="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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103
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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="nv" style="color: #008080;">rBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">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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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="scala"> <span class="nf" style="color: #900; font-weight: 600;">if</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="nv" style="color: #008080;">bc</span><span class="o" style="font-weight: 600;">.</span><span class="py">base</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">bcString</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"N"</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); 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="178" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -178,8 +178,8 @@ class Vcf(val file: File, val contigsWithSizes: List[(String, Int)] = Nil) {</td>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="scala"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">writeFixRecord</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;">fix</span><span class="k" style="font-weight: 600;">:</span> <span class="kt" style="color: #458; font-weight: 600;">GenomeRegion.Fix</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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179
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">loc</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">fix</span><span class="o" style="font-weight: 600;">.</span><span class="py">_1</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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180
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">rBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">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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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">ref</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rBase</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">fix</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">alt</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rBase</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">fix</span><span class="o" style="font-weight: 600;">.</span><span class="py">_3</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">ref</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="py"><span class="idiff right">toString</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">fix</span><span class="o" style="font-weight: 600;">.</span><span class="py">_2</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">alt</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="py"><span class="idiff right">toString</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">fix</span><span class="o" style="font-weight: 600;">.</span><span class="py">_3</span></span>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">svlen</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">alt</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">ref</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span></span>
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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">
184
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<td class="diff-line-num new_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">
184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">svend</span> <span class="k" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loc</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">ref</span><span class="o" style="font-weight: 600;">.</span><span class="py">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num old_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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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">svtype</span> <span class="k" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">svlen</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="s" style="color: #d14;">"DEL"</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"INS"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,7 +195,7 @@ class Vcf(val file: File, val contigsWithSizes: List[(String, Int)] = Nil) {</td>
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195
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<td class="diff-line-num new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">loc</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">dup</span><span class="o" style="font-weight: 600;">.</span><span class="py">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num 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="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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<pre style="margin: 0;"> <span id="LC196" class="line" lang="scala"> <span class="k" style="font-weight: 600;">val</span> <span class="nv" style="color: #008080;">rBase</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">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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<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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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="scala"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">line</span> <span class="k" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">region</span><span class="o" style="font-weight: 600;">.</span><span class="py">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tab</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;">tab</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;">tab</span></span>
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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
198
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<td class="diff-line-num new_line old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="scala"> <span class="n" style="color: #333;">line</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;">tab</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"<DUP>"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tab</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;">tab</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"PASS"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tab</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="scala"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: #008080;">rBase</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="py"><span class="idiff right">toString</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"<DUP>"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tab</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;">tab</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"PASS"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tab</span></span>
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199
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="scala"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"SVTYPE=DUP;SVLEN="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">dup</span><span class="o" style="font-weight: 600;">.</span><span class="py">size</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">";END="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">dup</span><span class="o" style="font-weight: 600;">.</span><span class="py">stop</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">";IMPRECISE"</span></span>
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200
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="scala"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"GT"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"./."</span></span>
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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
201
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="scala"> <span class="nv" style="color: #008080;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="py">println</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">)</span></span>
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