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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/trimmomatic">Debian Med / trimmomatic</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/trimmomatic/commit/d2edfdeaf8ed8883aebb02a251b04521b5a70c00">d2edfdea</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-22T17:28:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.38+dfsg</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#bdc348bf75801c527f51cdeddc8edf027f7ef35a">
build.xml
</a>
</li>
<li class="file-stats">
<a href="#ca0173e46cf6700bfa0b6bfd55aae9bf7545bf31">
src/org/usadellab/trimmomatic/TrimStats.java
</a>
</li>
<li class="file-stats">
<a href="#c3931e958bb9ede60c37ece03bc3370da6303479">
src/org/usadellab/trimmomatic/Trimmomatic.java
</a>
</li>
<li class="file-stats">
<a href="#46cc3d6d669c2c83411ec35f6c51bed84192a969">
src/org/usadellab/trimmomatic/TrimmomaticPE.java
</a>
</li>
<li class="file-stats">
<a href="#4e4a19d9079bb598fecc443bc1c283d3d1427191">
src/org/usadellab/trimmomatic/TrimmomaticSE.java
</a>
</li>
<li class="file-stats">
<a href="#eba1c0bbc1b4ef5e13c2e72003718ff766134d42">
<span class="new-file">
+
src/org/usadellab/trimmomatic/trim/BaseCountTrimmer.java
</span>
</a>
</li>
<li class="file-stats">
<a href="#6bf30c2404113e6bc6dfd68f73bf74946fdad769">
src/org/usadellab/trimmomatic/trim/TailCropTrimmer.java
</a>
</li>
<li class="file-stats">
<a href="#268a96b74a38a1eb93a0d923c0de4ba40ab8de1d">
src/org/usadellab/trimmomatic/trim/TrimmerFactory.java
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="bdc348bf75801c527f51cdeddc8edf027f7ef35a">
<a href="https://salsa.debian.org/med-team/trimmomatic/commit/d2edfdeaf8ed8883aebb02a251b04521b5a70c00#bdc348bf75801c527f51cdeddc8edf027f7ef35a"><strong>build.xml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="xml"><span class="nt" style="color: navy;"><project</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"Trimmomatic"</span> <span class="na" style="color: teal;">default=</span><span class="s" style="color: #d14;">"dist"</span> <span class="na" style="color: teal;">basedir=</span><span class="s" style="color: #d14;">"."</span><span class="nt" style="color: navy;">></span></span>
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"version"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"0.3<span class="idiff left right">6</span>"</span><span class="nt" style="color: navy;">/></span></span>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"version"</span> <span class="na" style="color: teal;">value=</span><span class="s" style="color: #d14;">"0.3<span class="idiff left right">8</span>"</span><span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="xml"> </span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"src"</span> <span class="na" style="color: teal;">location=</span><span class="s" style="color: #d14;">"src"</span> <span class="nt" style="color: navy;">/></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="xml"> <span class="nt" style="color: navy;"><property</span> <span class="na" style="color: teal;">name=</span><span class="s" style="color: #d14;">"lib"</span> <span class="na" style="color: teal;">location=</span><span class="s" style="color: #d14;">"lib"</span> <span class="nt" style="color: navy;">/></span></span>
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<li id="ca0173e46cf6700bfa0b6bfd55aae9bf7545bf31">
<a href="https://salsa.debian.org/med-team/trimmomatic/commit/d2edfdeaf8ed8883aebb02a251b04521b5a70c00#ca0173e46cf6700bfa0b6bfd55aae9bf7545bf31"><strong>src/org/usadellab/trimmomatic/TrimStats.java</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">usadellab</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">trimmomatic</span><span class="o" style="font-weight: 600;">;</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="java"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.File</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.IOException</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.io.PrintStream</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.text.DecimalFormat</span><span class="o" style="font-weight: 600;">;</span></span>
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4
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="java"></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC8" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.usadellab.trimmomatic.fastq.FastqRecord</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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,25 +11,25 @@ public class TrimStats</td>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="java"><span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">DecimalFormat</span> <span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">DecimalFormat</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"0.00"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">i</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">s</span>urvivingBoth</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">s</span>urvivingForward</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">s</span>urvivingReverse</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">readsI</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">readsS</span>urvivingBoth</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">readsS</span>urvivingForward</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">readsS</span>urvivingReverse</span><span class="o" style="font-weight: 600;">;</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">TrimStats</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">i</span>nput</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="LC19" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">s</span>urvivingBoth</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="LC20" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">s</span>urvivingForward</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="LC21" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">s</span>urvivingReverse</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="LC21" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsI</span>nput</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="LC22" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsS</span>urvivingBoth</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="LC23" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsS</span>urvivingForward</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="LC24" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsS</span>urvivingReverse</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="LC25" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">merge</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">TrimStats</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">input</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">i</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">survivingBoth</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">s</span>urvivingBoth</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">survivingForward</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">s</span>urvivingForward</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">survivingReverse</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">s</span>urvivingReverse</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">readsInput</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">readsI</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">readsSurvivingBoth</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">readsS</span>urvivingBoth</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">readsSurvivingForward</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">readsS</span>urvivingForward</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">readsSurvivingReverse</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="n" style="color: #333;"><span class="idiff">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">readsS</span>urvivingReverse</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="java"> </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">@@ -36,57 +39,79 @@ public class TrimStats</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">originalRecs</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">i</span>nput</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsI</span>nput</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recs</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">s</span>urvivingForward</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsS</span>urvivingForward</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">originalRecs</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="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">originalRecs</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">i</span>nput</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsI</span>nput</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recs</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recs</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">s</span>urvivingBoth</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsS</span>urvivingBoth</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">s</span>urvivingForward</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsS</span>urvivingForward</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java"> <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;">recs</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="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">s</span>urvivingReverse</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">readsS</span>urvivingReverse</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">getStatsSE</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="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">processStatsSE</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">PrintStream</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">statsSummaryStream</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dropped</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">input</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">s</span>urvivingForward</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dropped</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">readsInput</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">readsS</span>urvivingForward</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">survivingForwardPercent</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;"><span class="idiff left">survivingForward</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">droppedPercent</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;">dropped</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;"><span class="idiff left right">i</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">survivingForwardPercent</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;"><span class="idiff left">readsSurvivingForward</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="n" style="color: #333;"><span class="idiff right">readsI</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">droppedPercent</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;">dropped</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;"><span class="idiff left right">readsI</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Input Reads: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="s" style="color: #d14;">" Surviving: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">survivingForward</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingForwardPercent</span><span class="o" style="font-weight: 600;">)+</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Input Reads: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsInput</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Surviving Reads: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsSurvivingForward</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Surviving Read Percent: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingForwardPercent</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Dropped Reads: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dropped</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Dropped Read Percent: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">droppedPercent</span><span class="o" style="font-weight: 600;">));</span> </span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Input Reads: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsInput</span><span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> <span class="s" style="color: #d14;">" Surviving: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsSurvivingForward</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingForwardPercent</span><span class="o" style="font-weight: 600;">)+</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java"> <span class="s" style="color: #d14;">"%) Dropped: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dropped</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">droppedPercent</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="LC87" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">getStatsPE</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="LC89" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">processStatsPE</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">PrintStream</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">statsSummaryStream</span></span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dropped</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">input</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">survivingBoth</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">survivingForward</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">s</span>urvivingReverse</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dropped</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">readsInput</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">readsSurvivingBoth</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">readsSurvivingForward</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff right">readsS</span>urvivingReverse</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"> </span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">survivingBothPercent</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;"><span class="idiff left">survivingBoth</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">survivingForwardPercent</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;"><span class="idiff left">survivingForward</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">survivingReversePercent</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;"><span class="idiff left">survivingReverse</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">droppedPercent</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;">dropped</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;"><span class="idiff left right">i</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">survivingBothPercent</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;"><span class="idiff left">readsSurvivingBoth</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="n" style="color: #333;"><span class="idiff right">readsI</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">survivingForwardPercent</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;"><span class="idiff left">readsSurvivingForward</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="n" style="color: #333;"><span class="idiff right">readsI</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">survivingReversePercent</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;"><span class="idiff left">readsSurvivingReverse</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="n" style="color: #333;"><span class="idiff right">readsI</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">droppedPercent</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;">dropped</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;"><span class="idiff left right">readsI</span>nput</span><span class="o" style="font-weight: 600;">;</span></span>
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85
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java"></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Input Read Pairs: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">+</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="s" style="color: #d14;">" Both Surviving: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">survivingBoth</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingBothPercent</span><span class="o" style="font-weight: 600;">)+</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> <span class="s" style="color: #d14;">"%) Forward Only Surviving: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">survivingForward</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingForwardPercent</span><span class="o" style="font-weight: 600;">)+</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> <span class="s" style="color: #d14;">"%) Reverse Only Surviving: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">survivingReverse</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingReversePercent</span><span class="o" style="font-weight: 600;">)+</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Input Read Pairs: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsInput</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Both Surviving Reads: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsSurvivingBoth</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Both Surviving Read Percent: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingBothPercent</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Forward Only Surviving Reads: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsSurvivingForward</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="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Forward Only Surviving Read Percent: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingForwardPercent</span><span class="o" style="font-weight: 600;">));</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Reverse Only Surviving Reads: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsSurvivingReverse</span><span class="o" style="font-weight: 600;">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Reverse Only Surviving Read Percent: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingReversePercent</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="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Dropped Reads: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dropped</span><span class="o" style="font-weight: 600;">);</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Dropped Read Percent: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">droppedPercent</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="java"> <span class="o" style="font-weight: 600;">}</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> </span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"Input Read Pairs: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsInput</span><span class="o" style="font-weight: 600;">+</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="s" style="color: #d14;">" Both Surviving: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsSurvivingBoth</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingBothPercent</span><span class="o" style="font-weight: 600;">)+</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> <span class="s" style="color: #d14;">"%) Forward Only Surviving: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsSurvivingForward</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingForwardPercent</span><span class="o" style="font-weight: 600;">)+</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="s" style="color: #d14;">"%) Reverse Only Surviving: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">readsSurvivingReverse</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">survivingReversePercent</span><span class="o" style="font-weight: 600;">)+</span></span>
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90
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="java"> <span class="s" style="color: #d14;">"%) Dropped: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dropped</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;">formatter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">droppedPercent</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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91
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="java"></span>
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92
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<li id="c3931e958bb9ede60c37ece03bc3370da6303479">
<a href="https://salsa.debian.org/med-team/trimmomatic/commit/d2edfdeaf8ed8883aebb02a251b04521b5a70c00#c3931e958bb9ede60c37ece03bc3370da6303479"><strong>src/org/usadellab/trimmomatic/Trimmomatic.java</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">@@ -95,9 +95,9 @@ public class Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">showUsage</span><span class="o" style="font-weight: 600;">)</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="java"> <span class="o" style="font-weight: 600;">{</span></span>
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97
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Usage: "</span><span class="o" style="font-weight: 600;">);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>..."</span><span class="o" style="font-weight: 600;">);</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-<span class="idiff left right">summary <statsSummaryFile>] [-</span>quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>..."</span><span class="o" style="font-weight: 600;">);</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="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" or: "</span><span class="o" style="font-weight: 600;">);</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>..."</span><span class="o" style="font-weight: 600;">);</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-<span class="idiff left right">summary <statsSummaryFile>] [-</span>quiet] <inputFile> <outputFile> <trimmer1>..."</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="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" or: "</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="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" -version"</span><span class="o" style="font-weight: 600;">);</span> </span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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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<li id="46cc3d6d669c2c83411ec35f6c51bed84192a969">
<a href="https://salsa.debian.org/med-team/trimmomatic/commit/d2edfdeaf8ed8883aebb02a251b04521b5a70c00#46cc3d6d669c2c83411ec35f6c51bed84192a969"><strong>src/org/usadellab/trimmomatic/TrimmomaticPE.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,7 +50,7 @@ public class TrimmomaticPE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processSingleThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">FastqParser</span> <span class="n" style="color: #333;">parser1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqParser</span> <span class="n" style="color: #333;">parser2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer1P</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java"> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer1U</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer2P</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer2U</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[],</span> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">PairingValidator</span> <span class="n" style="color: #333;">pairingValidator</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[],</span> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">P<span class="idiff left">rintStream</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">statsSummaryStream</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">P</span>airingValidator</span> <span class="n" style="color: #333;">pairingValidator</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"> <span class="n" style="color: #333;">TrimStats</span> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TrimStats</span><span class="o" style="font-weight: 600;">();</span></span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,12 +115,13 @@ public class TrimmomaticPE extends Trimmomatic</td>
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115
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stats</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left">getStatsPE</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="LC118" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stats</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left">processStatsPE</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">statsSummaryStream</span></span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processMultiThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">FastqParser</span> <span class="n" style="color: #333;">parser1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqParser</span> <span class="n" style="color: #333;">parser2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer1P</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer1U</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer2P</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer2U</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="java"> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[],</span> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">PairingValidator</span> <span class="n" style="color: #333;">pairingValidator</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[],</span> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"> <span class="n" style="color: #333;">PairingValidator</span> <span class="n" style="color: #333;">pairingValidator</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FastqRecord</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">parser1Queue</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FastqRecord</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="LC127" class="line" lang="java"> <span class="n" style="color: #333;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FastqRecord</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">parser2Queue</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FastqRecord</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -249,7 +250,7 @@ public class TrimmomaticPE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="java"> <span class="n" style="color: #333;">trimLogThread</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">join</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="java"> <span class="n" style="color: #333;">statsThread</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">join</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsWorker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStats</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;"><span class="idiff left">getStatsPE</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="LC253" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsWorker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStats</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;"><span class="idiff left">processStatsPE</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">statsSummaryStream</span></span><span class="o" style="font-weight: 600;">));</span></span>
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253
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">InterruptedException</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span></span>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="java"> <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="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -258,7 +259,7 @@ public class TrimmomaticPE extends Trimmomatic</td>
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258
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="java"></span>
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">process</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">input1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">input2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">output1P</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">output1U</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">output2P</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">output2U</span><span class="o" style="font-weight: 600;">,</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="java"> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">phredOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">trimLog</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">validatePairing</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="java"> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">phredOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">trimLog</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">File</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">statsSummaryFile</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">validatePairing</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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262
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="java"> <span class="n" style="color: #333;">FastqParser</span> <span class="n" style="color: #333;">parser1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastqParser</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phredOffset</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="java"> <span class="n" style="color: #333;">parser1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">parse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">input1</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="302" style="width: 35px; color: rgba(0,0,0,0.3); 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="303" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -302,6 +303,10 @@ public class TrimmomaticPE extends Trimmomatic</td>
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302
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// FileOutputStream(trimLog),1000000),false);</span></span>
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303
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="java"> <span class="n" style="color: #333;">trimLogStream</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PrintStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trimLog</span><span class="o" style="font-weight: 600;">);</span></span>
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="java"> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">statsSummaryStream</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsSummaryFile</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PrintStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsSummaryFile</span><span class="o" style="font-weight: 600;">);</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="java"> <span class="n" style="color: #333;">PairingValidator</span> <span class="n" style="color: #333;">pairingValidator</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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306
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="java"> </span>
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">validatePairing</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="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -309,10 +314,10 @@ public class TrimmomaticPE extends Trimmomatic</td>
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309
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</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 class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>
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311
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="java"> <span class="n" style="color: #333;">processSingleThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">parser2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer1P</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer1U</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer2P</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer2U</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="java"> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pairingValidator</span><span class="o" style="font-weight: 600;">);</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="java"> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">statsSummaryStream</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">pairingValidator</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="java"> <span class="nf" style="color: #900; font-weight: 600;">processMultiThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">parser2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer1P</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer1U</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer2P</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer2U</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="java"> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pairingValidator</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="LC320" class="line" lang="java"> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">statsSummaryStream</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">pairingValidator</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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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="java"> <span class="n" style="color: #333;">serializer1P</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="java"> <span class="n" style="color: #333;">serializer1U</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">close</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="321" style="width: 35px; color: rgba(0,0,0,0.3); 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="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -321,6 +326,9 @@ public class TrimmomaticPE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trimLogStream</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" 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="java"> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsSummaryStream</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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325
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="java"> </span>
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326
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getFileExtensionIndex</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">str</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -414,6 +422,7 @@ public class TrimmomaticPE extends Trimmomatic</td>
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414
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">showVersion</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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415
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="java"> </span>
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416
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="java"> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">trimLog</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="java"> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">statsSummary</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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417
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="java"></span>
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="java"> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nonOptionArgs</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ArrayList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">>();</span></span>
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419
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="java"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); 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="445" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -436,6 +445,13 @@ public class TrimmomaticPE extends Trimmomatic</td>
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436
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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437
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446
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="java"> <span class="n" style="color: #333;">badOption</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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438
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447
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="java"> <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;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-summary"</span><span class="o" style="font-weight: 600;">))</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">argIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">)</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="java"> <span class="n" style="color: #333;">statsSummary</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">argIndex</span><span class="o" style="font-weight: 600;">++]);</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="java"> <span class="n" style="color: #333;">badOption</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="LC454" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="java"> <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;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-basein"</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">argIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</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">@@ -536,7 +552,8 @@ public class TrimmomaticPE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="java"> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[]=</span><span class="n" style="color: #333;">createTrimmers</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nonOptionArgsIter</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="java"> <span class="n" style="color: #333;">TrimmomaticPE</span> <span class="n" style="color: #333;">tm</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TrimmomaticPE</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="java"> <span class="n" style="color: #333;">tm</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">process</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">inputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">inputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">outputs</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;">outputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">phredOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimLog</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">validatePairs</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="LC555" class="line" lang="java"> <span class="n" style="color: #333;">tm</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">process</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">inputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">inputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">outputs</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;">outputs</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">],</span> </span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="java"> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">phredOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimLog</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">statsSummary</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">validatePairs</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="LC557" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"TrimmomaticPE: Completed successfully"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -546,8 +563,7 @@ public class TrimmomaticPE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span></span>
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550
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Usage: TrimmomaticPE [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>..."</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Usage: [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>..."</span><span class="o" style="font-weight: 600;">);</span></span>
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551
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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="LC568" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<li id="4e4a19d9079bb598fecc443bc1c283d3d1427191">
<a href="https://salsa.debian.org/med-team/trimmomatic/commit/d2edfdeaf8ed8883aebb02a251b04521b5a70c00#4e4a19d9079bb598fecc443bc1c283d3d1427191"><strong>src/org/usadellab/trimmomatic/TrimmomaticSE.java</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">@@ -48,7 +48,7 @@ public class TrimmomaticSE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java"></span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processSingleThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">FastqParser</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[],</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PrintStream</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">statsSummaryStream</span></span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java"> <span class="n" style="color: #333;">TrimStats</span> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TrimStats</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"></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">@@ -102,11 +102,11 @@ public class TrimmomaticSE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java"> <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="java"></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stats</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left">getStatsSE</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="LC105" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stats</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left">processStatsSE</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">statsSummaryStream</span></span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="java"> <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="java"></span>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">processMultiThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">FastqParser</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FastqSerializer</span> <span class="n" style="color: #333;">serializer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</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="java"> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">PrintStream</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">statsSummaryStream</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="java"> <span class="n" style="color: #333;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FastqRecord</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">parserQueue</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FastqRecord</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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112
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="java"> <span class="n" style="color: #333;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Runnable</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">taskQueue</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Runnable</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 class="mi" style="color: #099;">2</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="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -181,7 +181,7 @@ public class TrimmomaticSE extends Trimmomatic</td>
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181
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="java"> <span class="n" style="color: #333;">trimLogThread</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">join</span><span class="o" style="font-weight: 600;">();</span></span>
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182
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="java"></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="java"> <span class="n" style="color: #333;">statsThread</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">join</span><span class="o" style="font-weight: 600;">();</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsWorker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStats</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;"><span class="idiff left">getStatsSE</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">(</span>));</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsWorker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getStats</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;"><span class="idiff left">processStatsSE</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">statsSummaryStream</span></span><span class="o" style="font-weight: 600;">));</span></span>
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185
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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186
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">InterruptedException</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span></span>
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187
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="java"> <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="190" style="width: 35px; color: rgba(0,0,0,0.3); 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="190" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -190,7 +190,7 @@ public class TrimmomaticSE extends Trimmomatic</td>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="java"></span>
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191
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">process</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">phredOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">trimLog</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</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="LC193" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">process</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[],</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">phredOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">trimLog</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">File</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">statsSummaryFile</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</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="LC194" class="line" lang="java"> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="java"> <span class="n" style="color: #333;">FastqParser</span> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastqParser</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phredOffset</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="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -218,15 +218,22 @@ public class TrimmomaticSE extends Trimmomatic</td>
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trimLog</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="java"> <span class="n" style="color: #333;">trimLogStream</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PrintStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trimLog</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="java"> <span class="n" style="color: #333;">PrintStream</span> <span class="n" style="color: #333;">statsSummaryStream</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsSummaryFile</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PrintStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsSummaryFile</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</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 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="LC222" class="line" lang="java"> <span class="n" style="color: #333;">processSingleThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="java"> <span class="n" style="color: #333;">processSingleThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">statsSummaryStream</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="java"> <span class="nf" style="color: #900; font-weight: 600;">processMultiThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimLogStream</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="LC228" class="line" lang="java"> <span class="nf" style="color: #900; font-weight: 600;">processMultiThreaded</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">serializer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">statsSummaryStream</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </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="LC229" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java"> <span class="n" style="color: #333;">serializer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trimLogStream</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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229
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="java"> <span class="n" style="color: #333;">trimLogStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">statsSummaryStream</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="java"> <span class="n" style="color: #333;">statsSummaryStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">IOException</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -238,6 +245,7 @@ public class TrimmomaticSE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">badOption</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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239
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="java"></span>
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="java"> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">trimLog</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="java"> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">statsSummary</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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241
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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242
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">showVersion</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span> </span>
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -262,6 +270,13 @@ public class TrimmomaticSE extends Trimmomatic</td>
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262
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="java"> <span class="n" style="color: #333;">badOption</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="LC272" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="java"> <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;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-summary"</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">argIndex</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="java"> <span class="n" style="color: #333;">statsSummary</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">argIndex</span><span class="o" style="font-weight: 600;">++]);</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="java"> <span class="n" style="color: #333;">badOption</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="LC279" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="java"> <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;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-quiet"</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="java"> <span class="n" style="color: #333;">quiet</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="LC282" class="line" lang="java"> <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;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-version"</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="303" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -303,7 +318,7 @@ public class TrimmomaticSE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="java"> <span class="n" style="color: #333;">Trimmer</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">[]=</span><span class="n" style="color: #333;">createTrimmers</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nonOptionArgsIter</span><span class="o" style="font-weight: 600;">);</span></span>
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="java"></span>
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305
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="java"> <span class="n" style="color: #333;">TrimmomaticSE</span> <span class="n" style="color: #333;">tm</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TrimmomaticSE</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">);</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="java"> <span class="n" style="color: #333;">tm</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">process</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">phredOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimLog</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="LC321" class="line" lang="java"> <span class="n" style="color: #333;">tm</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">process</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">input</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimmers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">phredOffset</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">trimLog</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">statsSummary</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </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="LC322" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="java"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">infoln</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"TrimmomaticSE: Completed successfully"</span><span class="o" style="font-weight: 600;">);</span></span>
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309
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -314,7 +329,7 @@ public class TrimmomaticSE extends Trimmomatic</td>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">err</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Usage: TrimmomaticSE [-<span class="idiff left right">threads <threads>] [-phred33|-phred64] [-trimlog <trimLog</span>File>] [-quiet] <inputFile> <outputFile> <trimmer1>..."</span><span class="o" style="font-weight: 600;">);</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Usage: TrimmomaticSE [-<span class="idiff left right">version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummary</span>File>] [-quiet] <inputFile> <outputFile> <trimmer1>..."</span><span class="o" style="font-weight: 600;">);</span></span>
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318
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="java"> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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="LC334" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<li id="eba1c0bbc1b4ef5e13c2e72003718ff766134d42">
<a href="https://salsa.debian.org/med-team/trimmomatic/commit/d2edfdeaf8ed8883aebb02a251b04521b5a70c00#eba1c0bbc1b4ef5e13c2e72003718ff766134d42"><strong>src/org/usadellab/trimmomatic/trim/BaseCountTrimmer.java</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">org</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">usadellab</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">trimmomatic</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">trim</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.BitSet</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">org.usadellab.trimmomatic.fastq.FastqRecord</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BaseCountTrimmer</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">AbstractSingleRecordTrimmer</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="java"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minCount</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="LC9" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">Integer</span> <span class="n" style="color: #333;">maxCount</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">BitSet</span> <span class="n" style="color: #333;">baseSet</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">BaseCountTrimmer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="java"> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">split</span><span class="o" style="font-weight: 600;">[]=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"> <span class="n" style="color: #333;">baseSet</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BitSet</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="java"> </span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">split</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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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"> </span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="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;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">charAt</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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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java"> <span class="n" style="color: #333;">baseSet</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="java"> </span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">split</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span> </span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="java"> <span class="n" style="color: #333;">minCount</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">split</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="LC28" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">split</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="java"> <span class="n" style="color: #333;">maxCount</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">split</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="LC31" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">FastqRecord</span> <span class="nf" style="color: #900; font-weight: 600;">processRecord</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">FastqRecord</span> <span class="n" style="color: #333;">in</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</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="LC39" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="java"> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">in</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequence</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="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;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">charAt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">baseSet</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java"> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">++;</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java"> </span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">minCount</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> </span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">maxCount</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">maxCount</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">in</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<li id="6bf30c2404113e6bc6dfd68f73bf74946fdad769">
<a href="https://salsa.debian.org/med-team/trimmomatic/commit/d2edfdeaf8ed8883aebb02a251b04521b5a70c00#6bf30c2404113e6bc6dfd68f73bf74946fdad769"><strong>src/org/usadellab/trimmomatic/trim/TailCropTrimmer.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<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">@@ -12,7 +12,7 @@ public class TailCropTrimmer extends AbstractSingleRecordTrimmer</td>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="java"> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">arg</span><span class="o" style="font-weight: 600;">[]=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java"> </span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="java"> <span class="n" style="color: #333;">bases</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arg</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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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="java"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="java"> <span class="idiff left right"> </span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</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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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="java"> <span class="n" style="color: #333;">maxLength</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">arg</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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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/trimmomatic/commit/d2edfdeaf8ed8883aebb02a251b04521b5a70c00#268a96b74a38a1eb93a0d923c0de4ba40ab8de1d"><strong>src/org/usadellab/trimmomatic/trim/TrimmerFactory.java</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">@@ -60,6 +60,9 @@ public class TrimmerFactory</td>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="java"> </span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trimmerName</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"AVGQUAL"</span><span class="o" style="font-weight: 600;">))</span></span>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">AvgQualTrimmer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trimmerName</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"BASECOUNT"</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">BaseCountTrimmer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">);</span></span>
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63
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"> </span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">trimmerName</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"TOPHRED33"</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">ToPhred33Trimmer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">);</span></span>
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