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<h3>

Andreas Tille pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968">2d8023c3</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-01-11T21:51:59Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.18.23+dfsg</pre>

</li>

</ul>

<h4>28 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#89581ac0b61dde434443cdf65afd6f4e5f19399d">

src/main/java/picard/analysis/directed/RnaSeqMetricsCollector.java

</a>

</li>

<li class="file-stats">

<a href="#6a02930b07b9a5d4b76685f51390584d3d138f67">

src/main/java/picard/illumina/IlluminaBasecallsToFastq.java

</a>

</li>

<li class="file-stats">

<a href="#4e3534a75dfd4f65811dba40ad728ca9e29c2844">

src/main/java/picard/illumina/IlluminaBasecallsToSam.java

</a>

</li>

<li class="file-stats">

<a href="#776518b1ba71a408ae21f8028798a4177a07da9a">

src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java

</a>

</li>

<li class="file-stats">

<a href="#c3739150012b3ae914edffdb52e1e5d9f670f249">

src/main/java/picard/illumina/parser/BaseIlluminaDataProvider.java

</a>

</li>

<li class="file-stats">

<a href="#d6bb75c9024cc453664c0b86f81e99351b1b0cfe">

src/main/java/picard/illumina/parser/CbclData.java

</a>

</li>

<li class="file-stats">

<a href="#42ffd9ee8bcca3205d789b07350058144442f1ff">

src/main/java/picard/illumina/parser/FilterParser.java

</a>

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<li class="file-stats">

<a href="#3d226ee21322a8c38428ca7889d26099c1bac15d">

src/main/java/picard/illumina/parser/IlluminaData.java

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<li class="file-stats">

<a href="#f55c3e150599eac421c9c0da2d34e9add32b8f31">

src/main/java/picard/illumina/parser/MultiTileFilterParser.java

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<li class="file-stats">

<a href="#db3e4fed95085a2dc452476c200f06c594ffe019">

src/main/java/picard/illumina/parser/readers/CbclReader.java

</a>

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<li class="file-stats">

<a href="#2251ea850ba98345bce132efaf72cb3836941ddb">

src/main/java/picard/sam/markduplicates/UmiUtil.java

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<li class="file-stats">

<a href="#dc629c42db1f7d3a87978e3c165dbd25e8d1cd12">

src/main/java/picard/sam/markduplicates/util/OpticalDuplicateFinder.java

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<li class="file-stats">

<a href="#7b8c8bdd576e9d3a0df135db87180469ffbaea30">

src/main/java/picard/sam/util/ReadNameParser.java

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<li class="file-stats">

<a href="#813710362f32b1c12d752ba7601a00d9dcbdbd1d">

src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java

</a>

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<li class="file-stats">

<a href="#12247ce6b4d138b1a549e9a057275fa85001fab8">

src/test/java/picard/analysis/CollectRnaSeqMetricsTest.java

</a>

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<li class="file-stats">

<a href="#4a3455d3b3da89fba102450e92ca3771afab474e">

src/test/java/picard/illumina/CollectIlluminaBasecallingMetricsTest.java

</a>

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<li class="file-stats">

<a href="#e1b7610ac081822bc869b241576e7cb24565e95a">

src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java

</a>

</li>

<li class="file-stats">

<a href="#916509529fd4b66c5557838d020d201d6b9921b7">

src/test/java/picard/illumina/parser/FilterParserTest.java

</a>

</li>

<li class="file-stats">

<a href="#47042314502a41f6758d5d534f7b8f4d1e996450">

src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.java

</a>

</li>

<li class="file-stats">

<a href="#754eaac80aeed7cf98a70fd23c33ca436613b0cc">

src/test/java/picard/sam/markduplicates/UmiUtilTest.java

</a>

</li>

<li class="file-stats">

<a href="#3c44e3e5eb22a09e90c4c23b3232c2fdda56ac9d">

testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz

</a>

</li>

<li class="file-stats">

<a href="#971a7324d3259fbd2bc1abe13be49e918c57d477">

testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/s_1_1102_barcode.txt.gz

</a>

</li>

<li class="file-stats">

<a href="#be3c2bcd0d53d74bb9e870efd33f725010a5708d">

testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.1.fastq

</a>

</li>

<li class="file-stats">

<a href="#b5aec946ccfb0c854b9094ba2bccab5bd883a645">

testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.2.fastq

</a>

</li>

<li class="file-stats">

<a href="#0b36bda2a264efe61db7b14ff0b709022f11e824">

testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.barcode_1.fastq

</a>

</li>

<li class="file-stats">

<a href="#8506191367e07f8a80c6a0d9b26eb280edb3ac94">

testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.barcode_2.fastq

</a>

</li>

<li class="file-stats">

<a href="#3aadcdc6893bc7af006edf8906d071b5dc87b7d3">

testdata/picard/illumina/151T8B8B151T_cbcl/sams/1102.NN.sam

</a>

</li>

<li class="file-stats">

<a href="#e5f7bc4229f0f1ed297e3bf5c17fa7773b2e182d">

testdata/picard/illumina/151T8B8B151T_cbcl/sams/NN.sam

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="89581ac0b61dde434443cdf65afd6f4e5f19399d">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#89581ac0b61dde434443cdf65afd6f4e5f19399d"><strong>src/main/java/picard/analysis/directed/RnaSeqMetricsCollector.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,7 +40,7 @@ public class RnaSeqMetricsCollector extends SAMRecordMultiLevelCollector<RnaSeqM</td>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">OverlapDetector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Gene</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">geneOverlapDetector</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">OverlapDetector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ribosomalSequenceOverlapDetector</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">collectCoverageStatistics</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"><span class="idiff left right">    </span></span>

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

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(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="44" style="width: 35px; color: rgba(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="LC44" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">RnaSeqMetricsCollector</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">MetricAccumulationLevel</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">accumulationLevels</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SAMReadGroupRecord</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">samRgRecords</span><span class="o" style="font-weight: 600;">,</span></span>

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

45

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

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java">                                  <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Long</span> <span class="n" style="color: #333;">ribosomalBasesInitialValue</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">OverlapDetector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Gene</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">geneOverlapDetector</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">OverlapDetector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ribosomalSequenceOverlapDetector</span><span class="o" style="font-weight: 600;">,</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java">                                  <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">HashSet</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="n" style="color: #333;">ignoredSequenceIndices</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minimumLength</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">StrandSpecificity</span> <span class="n" style="color: #333;">strandSpecificity</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="167" style="width: 35px; color: rgba(0,0,0,0.3); 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="167" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -167,8 +167,7 @@ public class RnaSeqMetricsCollector extends SAMRecordMultiLevelCollector<RnaSeqM</td>

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<pre style="margin: 0;"> <span id="LC167" 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="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" 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;">intersectionLength</span><span class="o" style="font-weight: 600;">/(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">)</span><span class="n" style="color: #333;">fragmentInterval</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="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">rrnaFragmentPercentage</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="java">                    <span class="c1" style="color: #998; font-style: italic;">// Assume entire read is ribosomal.</span></span>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java">                    <span class="c1" style="color: #998; font-style: italic;">// TODO: Should count reads, not bases?</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="java">                    <span class="n" style="color: #333;">metrics</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">RIBOSOMAL_BASES</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getReadLength</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java">                    <span class="n" style="color: #333;">metrics</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">RIBOSOMAL_BASES</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">getNumAlignedBases</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java">                    <span class="n" style="color: #333;">metrics</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PF_ALIGNED_BASES</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">getNumAlignedBases</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="java">                    <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

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<br>

</li>

<li id="6a02930b07b9a5d4b76685f51390584d3d138f67">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#6a02930b07b9a5d4b76685f51390584d3d138f67"><strong>src/main/java/picard/illumina/IlluminaBasecallsToFastq.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -281,7 +281,7 @@ public class IlluminaBasecallsToFastq extends CommandLineProgram {</td>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="java">                    <span class="n" style="color: #333;">FIRST_TILE</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">TILE_LIMIT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">queryNameComparator</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;">new</span> <span class="nf" style="color: #900; font-weight: 600;">FastqRecordsForClusterCodec</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readStructure</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">templates</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="diff-line-num old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="java">                            <span class="n" style="color: #333;">readStructure</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sampleBarcodes</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;">readStructure</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">molecularBarcode</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="diff-line-num old old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="java">                    <span class="n" style="color: #333;">FastqRecordsForCluster</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">class</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bclQualityEvaluationStrategy</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">I<span class="idiff left">NCLUDE_NON_PF_READS</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">I</span>GNORE_UNEXPECTED_BARCODES</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="java">                    <span class="n" style="color: #333;">FastqRecordsForCluster</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">class</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bclQualityEvaluationStrategy</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">IGNORE_UNEXPECTED_BARCODES</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="285" style="width: 35px; color: rgba(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="LC285" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="java">            <span class="n" style="color: #333;">basecallsConverter</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">IlluminaBasecallsConverter</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">BASECALLS_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">BARCODES_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">LANE</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readStructure</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="java">                    <span class="n" style="color: #333;">sampleBarcodeFastqWriterMap</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">demultiplex</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</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;">MAX_READS_IN_RAM_PER_TILE</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">readsPerCluster</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">TMP_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">NUM_PROCESSORS</span><span class="o" style="font-weight: 600;">,</span></span>

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<li id="4e3534a75dfd4f65811dba40ad728ca9e29c2844">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#4e3534a75dfd4f65811dba40ad728ca9e29c2844"><strong>src/main/java/picard/illumina/IlluminaBasecallsToSam.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); 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="312" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -312,7 +312,7 @@ public class IlluminaBasecallsToSam extends CommandLineProgram {</td>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="java">                    <span class="n" style="color: #333;">TMP_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">NUM_PROCESSORS</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="java">                    <span class="n" style="color: #333;">FIRST_TILE</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">TILE_LIMIT</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">QueryNameComparator</span><span class="o" style="font-weight: 600;">(),</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="java">                    <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">Codec</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">numOutputRecords</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;">SAMRecordsForCluster</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">class</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bclQualityEvaluationStrategy</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">I<span class="idiff left">NCLUDE_NON_PF_READS</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">I</span>GNORE_UNEXPECTED_BARCODES</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;">SAMRecordsForCluster</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">class</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bclQualityEvaluationStrategy</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">IGNORE_UNEXPECTED_BARCODES</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="java">            <span class="n" style="color: #333;">basecallsConverter</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">IlluminaBasecallsConverter</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">BASECALLS_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">BARCODES_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">LANE</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readStructure</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="n" style="color: #333;">barcodeSamWriterMap</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">MAX_READS_IN_RAM_PER_TILE</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">numOutputRecords</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">TMP_DIR</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">NUM_PROCESSORS</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">FORCE_GC</span><span class="o" style="font-weight: 600;">,</span></span>

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<li id="776518b1ba71a408ae21f8028798a4177a07da9a">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#776518b1ba71a408ae21f8028798a4177a07da9a"><strong>src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,9 +14,11 @@ import picard.illumina.parser.ReadStructure;</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">picard.illumina.parser.readers.AbstractIlluminaPositionFileReader</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">picard.illumina.parser.readers.BclQualityEvaluationStrategy</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">picard.illumina.parser.readers.LocsFileReader</span><span class="o" style="font-weight: 600;">;</span></span>

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">picard.util.ThreadPoolExecutorUtil</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">picard.util.ThreadPoolExecutorWithExceptions</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.time.Duration</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>

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

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Collections</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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,9 +26,7 @@ import java.util.Comparator;</td>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashMap</span><span class="o" style="font-weight: 600;">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.List</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Map</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.ConcurrentHashMap</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.ThreadPoolExecutor</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.TimeUnit</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.regex.Matcher</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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.regex.Pattern</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="java"></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,12 +36,10 @@ public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Baseca</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AbstractIlluminaPositionFileReader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PositionInfo</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">locs</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>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">filterFiles</span><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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ThreadPoolExecutorWithExceptions</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">barcodeWriterThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashMap</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 class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Map</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="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RecordWriter</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">completedWork</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Collections</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">synchronizedMap</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashMap</span><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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Map</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="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">barcodesFiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashMap</span><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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">includeNonPfReads</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="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * Constructor setting includeNonPfReads to true by default.</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     *</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param basecallsDir             Where to read basecalls from.</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param barcodesDir              Where to read barcodes from (optional; use basecallsDir if not specified).</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param lane                     What lane to process.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,52 +71,11 @@ public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Baseca</td>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Class</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CLUSTER_OUTPUT_RECORD</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">outputRecordClass</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="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">BclQualityEvaluationStrategy</span> <span class="n" style="color: #333;">bclQualityEvaluationStrategy</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="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">ignoreUnexpectedBarcodes</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">basecallsDir</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">barcodesDir</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">lane</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readStructure</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">barcodeRecordWriterMap</span><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;">demultiplex</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxReadsInRamPerTile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tmpDirs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numProcessors</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">firstTile</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;">tileLimit</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">outputRecordComparator</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">codecPrototype</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">outputRecordClass</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;">bclQualityEvaluationStrategy</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ignoreUnexpectedBarcodes</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="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param basecallsDir             Where to read basecalls from.</span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param barcodesDir              Where to read barcodes from (optional; use basecallsDir if not specified).</span></span>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param lane                     What lane to process.</span></span>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param readStructure            How to interpret each cluster.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param barcodeRecordWriterMap   Map from barcode to CLUSTER_OUTPUT_RECORD writer.  If demultiplex is false, must contain</span></span>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     *                                 one writer stored with key=null.</span></span>

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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param demultiplex              If true, output is split by barcode, otherwise all are written to the same output stream.</span></span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param maxReadsInRamPerTile     Configures number of reads each tile will store in RAM before spilling to disk.</span></span>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param tmpDirs                  For SortingCollection spilling.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param numProcessors            Controls number of threads.  If <= 0, the number of threads allocated is</span></span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     *                                 available cores - numProcessors.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param firstTile                (For debugging) If non-null, start processing at this tile.</span></span>

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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param tileLimit                (For debugging) If non-null, process no more than this many tiles.</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param outputRecordComparator   For sorting output records within a single tile.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param codecPrototype           For spilling output records to disk.</span></span>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param outputRecordClass        Inconveniently needed to create SortingCollections.</span></span>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param includeNonPfReads        If true, will include ALL reads (including those which do not have PF set)</span></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param ignoreUnexpectedBarcodes If true, will ignore reads whose called barcode is not found in barcodeRecordWriterMap,</span></span>

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">NewIlluminaBasecallsConverter</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">basecallsDir</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">barcodesDir</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lane</span><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="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ReadStructure</span> <span class="n" style="color: #333;">readStructure</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">?</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">ConvertedClusterDataWriter</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CLUSTER_OUTPUT_RECORD</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">barcodeRecordWriterMap</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">demultiplex</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="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxReadsInRamPerTile</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tmpDirs</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numProcessors</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Integer</span> <span class="n" style="color: #333;">firstTile</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Integer</span> <span class="n" style="color: #333;">tileLimit</span><span class="o" style="font-weight: 600;">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Comparator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CLUSTER_OUTPUT_RECORD</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">outputRecordComparator</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">SortingCollection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">Codec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CLUSTER_OUTPUT_RECORD</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">codecPrototype</span><span class="o" style="font-weight: 600;">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Class</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CLUSTER_OUTPUT_RECORD</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">outputRecordClass</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">BclQualityEvaluationStrategy</span> <span class="n" style="color: #333;">bclQualityEvaluationStrategy</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">includeNonPfReads</span><span class="o" style="font-weight: 600;">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java">                                         <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">ignoreUnexpectedBarcodes</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java">        <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">barcodeRecordWriterMap</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxReadsInRamPerTile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tmpDirs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">codecPrototype</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">ignoreUnexpectedBarcodes</span><span class="o" style="font-weight: 600;">,</span></span>

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

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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(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="LC76" class="line" lang="java">                <span class="n" style="color: #333;">demultiplex</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">outputRecordComparator</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bclQualityEvaluationStrategy</span><span class="o" style="font-weight: 600;">,</span></span>

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

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<td class="diff-line-num new_line" data-linenumber="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="java">                <span class="n" style="color: #333;">outputRecordClass</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">numProcessors</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">IlluminaDataProviderFactory</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">basecallsDir</span><span class="o" style="font-weight: 600;">,</span></span>

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

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="java">                        <span class="n" style="color: #333;">barcodesDir</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">lane</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">readStructure</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bclQualityEvaluationStrategy</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">includeNonPfReads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">includeNonPfReads</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tiles</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>

</pre>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(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="LC81" class="line" lang="java">        <span class="n" style="color: #333;">barcodeRecordWriterMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">keySet</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">forEach</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">barcodeWriterThreads</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ThreadPoolExecutorWithExceptions</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)));</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -196,31 +153,26 @@ public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Baseca</td>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java">        <span class="n" style="color: #333;">completedWorkExecutor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">shutdown</span><span class="o" style="font-weight: 600;">();</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//thread by surface tile</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ThreadPoolExecutor</span> <span class="n" style="color: #333;">tileProcessingExecutor</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ThreadPoolExecutorWithExceptions</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">numThreads</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="java">        <span class="n" style="color: #333;">workChecker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setTileProcessingExecutor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ThreadPoolExecutorWithExceptions</span> <span class="n" style="color: #333;">tileProcessingExecutor</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ThreadPoolExecutorWithExceptions</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">numThreads</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="java">        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Integer</span> <span class="n" style="color: #333;">tile</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java">            <span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">submit</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TileProcessor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">barcodesFiles</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;">tile</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">workChecker</span></span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java">            <span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">submit</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TileProcessor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">barcodesFiles</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;">tile</span><span class="o" style="font-weight: 600;">)));</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="java"></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="java">        <span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">shutdown</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="java">        <span class="n" style="color: #333;">awaitThreadPoolTermination</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Reading executor"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="java">        <span class="n" style="color: #333;">awaitThreadPoolTermination</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Tile completion executor"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">completedWorkExecutor</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="java">        <span class="n" style="color: #333;">barcodeWriterThreads</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">values</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">forEach</span><span class="o" style="font-weight: 600;">(</span><span class="nl">ThreadPoolExecutor:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">shutdown</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java">        <span class="n" style="color: #333;">barcodeWriterThreads</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">forEach</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">executor</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">awaitThreadPoolTermination</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" writer"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">executor</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

215

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">awaitThreadPoolTermination</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">executorName</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ThreadPoolExecutor</span> <span class="n" style="color: #333;">executorService</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java">        <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java">            <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">executorService</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">awaitTermination</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;">TimeUnit</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">SECONDS</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="java">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</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="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"%s waiting for job completion. Finished jobs - %d : Running jobs - %d : Queued jobs  - %d"</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="java">                        <span class="n" style="color: #333;">executorName</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">executorService</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCompletedTaskCount</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">executorService</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getActiveCount</span><span class="o" style="font-weight: 600;">(),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="java">                        <span class="n" style="color: #333;">executorService</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getQueue</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">()));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

221

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</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 class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

223

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="java">            <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">printStackTrace</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

164

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java">        <span class="n" style="color: #333;">ThreadPoolExecutorUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">awaitThreadPoolTermination</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Reading executor"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Duration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ofMinutes</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

165

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

<pre style="margin: 0;">+<span id="LC165" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// if there was an exception reading then initiate an immediate shutdown.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC167" 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;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exception</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="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tasksStillRunning</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">completedWorkExecutor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">shutdownNow</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java">            <span class="n" style="color: #333;">tasksStillRunning</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">barcodeWriterThreads</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">values</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">stream</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">mapToLong</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">executor</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">executor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">shutdownNow</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">()).</span><span class="na" style="color: teal;">sum</span><span class="o" style="font-weight: 600;">();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">PicardException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Reading executor had exceptions. There were "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tasksStillRunning</span></span>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="java">                    <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" tasks were still running or queued and have been cancelled."</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">exception</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="java">            <span class="n" style="color: #333;">ThreadPoolExecutorUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">awaitThreadPoolTermination</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Tile completion executor"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">completedWorkExecutor</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Duration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ofMinutes</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">));</span></span>

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="java">            <span class="n" style="color: #333;">barcodeWriterThreads</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">values</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">forEach</span><span class="o" style="font-weight: 600;">(</span><span class="nl">ThreadPoolExecutor:</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">shutdown</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java">            <span class="n" style="color: #333;">barcodeWriterThreads</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">forEach</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">executor</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">ThreadPoolExecutorUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">awaitThreadPoolTermination</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" writer"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">executor</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Duration</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ofMinutes</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">)));</span></span>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="java"></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>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -249,16 +201,30 @@ public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Baseca</td>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Closer</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="n" style="color: #333;">Runnable</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ConvertedClusterDataWriter</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CLUSTER_OUTPUT_RECORD</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="nf" style="color: #900; font-weight: 600;">Closer</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ConvertedClusterDataWriter</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CLUSTER_OUTPUT_RECORD</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="java">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="java">        <span class="nd">@Override</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC214" 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;">run</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="java">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">debug</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Closing writer for barcode "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="java">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">writer</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>

</pre>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TileProcessor</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="n" style="color: #333;">Runnable</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tileNum</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">SortingCollection</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CLUSTER_OUTPUT_RECORD</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">barcodeToRecordCollection</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">HashMap</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">barcodeFile</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">CompletedWorkChecker</span> <span class="n" style="color: #333;">workChecker</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="LC258" class="line" lang="java">        <span class="n" style="color: #333;">TileProcessor</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tileNum</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">barcodeFile</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">CompletedWorkChecker</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">workChecker</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="java">        <span class="n" style="color: #333;">TileProcessor</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tileNum</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">barcodeFile</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="java">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tileNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tileNum</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;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">barcodeFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">barcodeFile</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="java">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">workChecker</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">workChecker</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="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="nd">@Override</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -268,12 +234,8 @@ public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Baseca</td>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="java">            <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dataProvider</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="java">                <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ClusterData</span> <span class="n" style="color: #333;">cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataProvider</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</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;">readProgressLogger</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">record</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="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="LC271" class="line" lang="java">                <span class="c1" style="color: #998; font-style: italic;">// If this cluster is passing, or we do NOT want to ONLY emit passing reads, then add it to</span></span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="java">                <span class="c1" style="color: #998; font-style: italic;">// the next</span></span>

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<pre style="margin: 0;">-<span id="LC273" 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;">cluster</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isPf</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">includeNonPfReads</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="java">                  <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">demultiplex</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">cluster</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMatchedBarcode</span><span class="o" style="font-weight: 600;">()</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="LC275" class="line" lang="java">                  <span class="n" style="color: #333;">addRecord</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">converter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">convertClusterToOutputRecord</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cluster</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="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="java">                <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">demultiplex</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">cluster</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMatchedBarcode</span><span class="o" style="font-weight: 600;">()</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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<td class="diff-line-num new new_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="java">                <span class="n" style="color: #333;">addRecord</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">converter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">convertClusterToOutputRecord</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cluster</span><span class="o" style="font-weight: 600;">));</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="java">            <span class="n" style="color: #333;">dataProvider</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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); 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="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -285,8 +247,7 @@ public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Baseca</td>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="java">                <span class="n" style="color: #333;">writerList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">RecordWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">));</span></span>

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

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="java">            <span class="o" style="font-weight: 600;">});</span></span>

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<td class="diff-line-num old old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="java">            <span class="n" style="color: #333;">workChecker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">registerCompletedWork</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tileNum</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">writerList</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="java">            <span class="n" style="color: #333;">completedWork</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tileNum</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">writerList</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;">log</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Finished processing tile "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tileNum</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC253" 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="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>

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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">@@ -314,21 +275,19 @@ public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Baseca</td>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="java">            <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxRecordsInRam</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;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</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;">maxReadsInRamPerTile</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="n" style="color: #333;">barcodeRecordWriterMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">SortingCollection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">newInstance</span><span class="o" style="font-weight: 600;">(</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">SortingCollection</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">newInstance<span class="idiff left right">FromPaths</span></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="n" style="color: #333;">outputRecordClass</span><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="n" style="color: #333;">codecPrototype</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">clone</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;">outputRecordComparator</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="n" style="color: #333;">maxRecordsInRam</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 class="n" style="color: #333;"><span class="idiff left right">tmpDirs</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="java">                    <span class="n" style="color: #333;"><span class="idiff left">IOUtil</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">filesToPaths</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpDirs</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="LC284" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CompletedWorkChecker</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="n" style="color: #333;">Runnable</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="java"></span>

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<td class="diff-line-num new_line old" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Map</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="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RecordWriter</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">completedWork</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ConcurrentHashMap</span><span class="o" style="font-weight: 600;"><>();</span></span>

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<pre style="margin: 0;"> <span id="LC290" 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;">currentTileIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="java">        <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">ThreadPoolExecutor</span> <span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="java">        <span class="nd">@Override</span></span>

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<td class="diff-line-num new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC293" 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;">run</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -337,30 +296,19 @@ public class NewIlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD> extends Baseca</td>

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<pre style="margin: 0;"> <span id="LC296" 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;">completedWork</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentTile</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="java">                    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">info</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing out tile "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">currentTile</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="java">                    <span class="n" style="color: #333;">completedWork</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;">currentTile</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">forEach</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">barcodeWriterThreads</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;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getBarcode</span><span class="o" style="font-weight: 600;">()).</span><span class="na" style="color: teal;">submit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">));</span></span>

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<td class="diff-line-num new_line old" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="java">                    <span class="n" style="color: #333;">completedWork</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentTile</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="java">                    <span class="n" style="color: #333;">currentTileIndex</span><span class="o" style="font-weight: 600;">++;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num old old_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC343" 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;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isTerminated</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">completedWork</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">()</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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<td class="diff-line-num new_line old" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="java">                    <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="java">                    <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="java">                        <span class="n" style="color: #333;">Thread</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">sleep</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">5000</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</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 class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="java">                        <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">PicardException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMessage</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">//we are all done scheduling work.. now schedule the closes</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="java">            <span class="n" style="color: #333;">barcodeRecordWriterMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">forEach</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="java">                <span class="n" style="color: #333;">ThreadPoolExecutorWithExceptions</span> <span class="n" style="color: #333;">executorService</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">barcodeWriterThreads</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;">barcode</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="java">                <span class="n" style="color: #333;">executorService</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">shutdown</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="java">                <span class="n" style="color: #333;">awaitThreadPoolTermination</span><span class="o" style="font-weight: 600;">(</span> <span class="s" style="color: #d14;">"Barcode writer ("</span>  <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">barcode</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;">executorService</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="java">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">debug</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Closing writer for barcode "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="java">                <span class="n" style="color: #333;">writer</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="java">            <span class="o" style="font-weight: 600;">});</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="java">            <span class="n" style="color: #333;">barcodeRecordWriterMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">forEach</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">barcodeWriterThreads</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;">barcode</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">submit</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Closer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">)));</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

357

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">registerCompletedWork</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;">tileNum</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;">RecordWriter</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">writerList</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="java">            <span class="n" style="color: #333;">completedWork</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tileNum</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">writerList</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new_line old" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setTileProcessingExecutor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ThreadPoolExecutor</span> <span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="java">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tileProcessingExecutor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tileProcessingExecutor</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>

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<br>

</li>

<li id="c3739150012b3ae914edffdb52e1e5d9f670f249">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#c3739150012b3ae914edffdb52e1e5d9f670f249"><strong>src/main/java/picard/illumina/parser/BaseIlluminaDataProvider.java</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,7 +42,7 @@ public abstract class BaseIlluminaDataProvider implements Iterator<ClusterData>,</td>

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

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(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="LC44" class="line" lang="java">    <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addData</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ClusterData</span> <span class="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">PfData</span> <span class="n" style="color: #333;">pfData</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

45

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<td class="diff-line-num new_line old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java">        <span class="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setPf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pfData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isPf<span class="idiff left right">Read</span></span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java">        <span class="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setPf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pfData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isPf</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>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java">    <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addData</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ClusterData</span> <span class="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">BarcodeData</span> <span class="n" style="color: #333;">barcodeData</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -72,9 +72,9 @@ public abstract class BaseIlluminaDataProvider implements Iterator<ClusterData>,</td>

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<pre style="margin: 0;"> <span id="LC72" 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;">numReads</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java">            <span class="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getRead</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="na" style="color: teal;">setQualities</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">qualities</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="LC74" class="line" lang="java">        <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="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setPf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cbclData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isPf<span class="idiff left right">Read</span></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="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setX</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cbclData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get<span class="idiff left">XCoordinate</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="LC77" class="line" lang="java">        <span class="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cbclData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get<span class="idiff left">YCoordinate</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="LC75" class="line" lang="java">        <span class="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setPf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cbclData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">isPf</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="n" style="color: #333;">clusterData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setX</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cbclData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get<span class="idiff left">PositionInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">().</span></span><span class="na" style="color: teal;"><span class="idiff right">xQseqCoord</span></span><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;">clusterData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setY</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cbclData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">get<span class="idiff left">PositionInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">().</span></span><span class="na" style="color: teal;"><span class="idiff right">yQseqCoord</span></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="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java">    <span class="kd" style="font-weight: 600;">abstract</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">seekToTile</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;">seekAfterFirstRead</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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</li>

<li id="d6bb75c9024cc453664c0b86f81e99351b1b0cfe">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#d6bb75c9024cc453664c0b86f81e99351b1b0cfe"><strong>src/main/java/picard/illumina/parser/CbclData.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">@@ -9,27 +9,30 @@ import picard.illumina.parser.readers.AbstractIlluminaPositionFileReader;</td>

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<pre style="margin: 0;"> <span id="LC9" 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;">CbclData</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">BclData</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="n" style="color: #333;">PfData</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">PositionalData</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="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">;</span></span>

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

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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="n" style="color: #333;">AbstractIlluminaPositionFileReader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PositionInfo</span> <span class="n" style="color: #333;">positionInfo</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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;">boolean</span> <span class="n" style="color: #333;">pfRead</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"></span>

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

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<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>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">CbclData</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">outputLengths</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;">tile</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="java">        <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">outputLengths</span><span class="o" style="font-weight: 600;">);</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">;</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="java"></span>

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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java">    <span class="c1" style="color: #998; font-style: italic;">//CBCLs currently only contain PF reads.</span></span>

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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="java">    <span class="nd">@Override</span></span>

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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPf</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

</td>

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

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

</pre>

</td>

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

20

</td>

<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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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="LC24" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getTile</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

21

</td>

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

25

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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="LC25" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tile</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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

26

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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="LC26" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

</td>

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

27

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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="LC27" class="line" lang="java"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="diff-line-num new_line old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC24" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">setPositionInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AbstractIlluminaPositionFileReader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">PositionInfo</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">positionInfo</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="diff-line-num new_line old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC25" class="line" lang="java">        <span class="k" style="font-weight: 600;"><span class="idiff left">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">positionInfo</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span> <span class="n" style="color: #333;">positionInfo</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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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="LC28" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;"><span class="idiff left">AbstractIlluminaPositionFileReader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">PositionInfo</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">getPositionInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">(</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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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="LC29" class="line" lang="java">        <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></span> <span class="n" style="color: #333;">positionInfo</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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

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

26

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

30

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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="LC30" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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

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

27

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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

<pre style="margin: 0;"> <span id="LC31" class="line" lang="java"></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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<td class="diff-line-num new_line old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC28" 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;">setP<span class="idiff left">fRead</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pfRead</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

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<td class="diff-line-num new_line old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC29" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">p<span class="idiff left">fRead</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pfRead</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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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="LC32" 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;">setP<span class="idiff left">ositionInfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">AbstractIlluminaPositionFileReader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">PositionInfo</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">positionInfo</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

33

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

<pre style="margin: 0;">+<span id="LC33" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">p<span class="idiff left">ositionInfo</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">positionInfo</span></span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

</td>

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

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

30

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

34

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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="LC34" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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

35

</td>

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

<pre style="margin: 0;"> <span id="LC35" class="line" lang="java"></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="java">    <span class="nd">@Override</span></span>

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

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(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="LC37" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getXCoordinate</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">positionInfo</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">xQseqCoord</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,9 +42,4 @@ public class CbclData extends BclData implements PfData, PositionalData {</td>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getYCoordinate</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">positionInfo</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">yQseqCoord</span><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="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num new_line old" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java">    <span class="nd">@Override</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPfRead</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pfRead</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>

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<br>

</li>

<li id="42ffd9ee8bcca3205d789b07350058144442f1ff">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#42ffd9ee8bcca3205d789b07350058144442f1ff"><strong>src/main/java/picard/illumina/parser/FilterParser.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); 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="65" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -65,7 +65,7 @@ class FilterParser extends PerTileParser<PfData> {</td>

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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;">PfData</span> <span class="nf" style="color: #900; font-weight: 600;">next</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java">                <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">nextValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><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="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;">PfData</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java">                    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPf<span class="idiff left right">Read</span></span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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68

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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="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPf</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(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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69

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java">                        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nextValue</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java">                <span class="o" style="font-weight: 600;">};</span></span>

</pre>

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<br>

</li>

<li id="3d226ee21322a8c38428ca7889d26099c1bac15d">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#3d226ee21322a8c38428ca7889d26099c1bac15d"><strong>src/main/java/picard/illumina/parser/IlluminaData.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); 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="59" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -59,7 +59,7 @@ interface RawIntensityData extends IlluminaData{</td>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

59

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="java"><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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="java"><span class="kd" style="font-weight: 600;">interface</span> <span class="nc" style="color: #458; font-weight: 600;">PfData</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">IlluminaData</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPf<span class="idiff left right">Read</span></span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPf</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>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(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="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"><span class="kd" style="font-weight: 600;">interface</span> <span class="nc" style="color: #458; font-weight: 600;">BarcodeData</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">IlluminaData</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<br>

</li>

<li id="f55c3e150599eac421c9c0da2d34e9add32b8f31">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#f55c3e150599eac421c9c0da2d34e9add32b8f31"><strong>src/main/java/picard/illumina/parser/MultiTileFilterParser.java</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +46,7 @@ public class MultiTileFilterParser extends MultiTileParser<PfData> {</td>

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

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

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">nextVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">();</span></span>

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

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

47

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<pre style="margin: 0;"> <span id="LC47" 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;">PfData</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java">            <span class="nd">@Override</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java">            <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPf<span class="idiff left right">Read</span></span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

49

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java">            <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPf</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

50

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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="n" style="color: #333;">nextVal</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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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(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="LC52" class="line" lang="java">        <span class="o" style="font-weight: 600;">};</span></span>

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<br>

</li>

<li id="db3e4fed95085a2dc452476c200f06c594ffe019">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#db3e4fed95085a2dc452476c200f06c594ffe019"><strong>src/main/java/picard/illumina/parser/readers/CbclReader.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); 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="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -200,13 +200,13 @@ public class CbclReader extends BaseBclReader implements CloseableIterator<CbclD</td>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="java">            <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">outputLength</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">outputLengths</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC202" 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;">cycle</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;">cycle</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">outputLength</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">cycle</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java">                    <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;"><span class="idiff left">TileData</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currentCycleTileInfo</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cycleData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">totalCycleCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: teal;"><span class="idiff right">tileInfo</span></span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="java">                    <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;"><span class="idiff left">CycleData</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">currentCycleData</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cycleData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">totalCycleCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>;</span></span>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="java">                    <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="java">                        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cachedTile</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">]</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="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC206" 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;">cachedFilter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c<span class="idiff left right">urrentCycleT</span>ileInfo</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tileNum</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="java">                                <span class="n" style="color: #333;">cacheFilterAndLocs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c<span class="idiff left right">urrentCycleT</span>ileInfo</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">locs</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC206" 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;">cachedFilter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">containsKey</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c<span class="idiff left">ycleData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">totalCycleCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: teal;"><span class="idiff right">t</span>ileInfo</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tileNum</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="java">                                <span class="n" style="color: #333;">cacheFilterAndLocs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">c<span class="idiff left">ycleData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">totalCycleCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: teal;"><span class="idiff right">t</span>ileInfo</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">locs</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="java">                            <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="java">                            <span class="n" style="color: #333;">cacheTile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">c<span class="idiff left right">urrentCycleTileInfo</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java">                            <span class="n" style="color: #333;">cacheTile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">c<span class="idiff left">ycleData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">totalCycleCount</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: teal;"><span class="idiff">tileInfo</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">currentCycleData</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="java">                        <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="java">                    <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">IOException</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="java">                        <span class="c1" style="color: #998; font-style: italic;">// when logging the error, increment cycle by 1, since totalCycleCount is zero-indexed but Illumina directories are 1-indexed.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -269,9 +269,7 @@ public class CbclReader extends BaseBclReader implements CloseableIterator<CbclD</td>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">advance</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">totalCycleCount</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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<td class="diff-line-num new_line old" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tileNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cycleData</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">tileInfo</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tileNum</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">CbclData</span> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CbclData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">outputLengths</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tileNum</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tilePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cachedTilePosition</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">totalCycleCount</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="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">CbclData</span> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CbclData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">outputLengths</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">cycleData</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: teal;">tileInfo</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tileNum</span><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>

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<pre style="margin: 0;"> <span id="LC274" 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;">read</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;">read</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">outputLengths</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;">read</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC275" 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;">cycle</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;">cycle</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">outputLengths</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">];</span> <span class="n" style="color: #333;">cycle</span><span class="o" style="font-weight: 600;">++)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -290,25 +288,31 @@ public class CbclReader extends BaseBclReader implements CloseableIterator<CbclD</td>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="java">                <span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">++;</span></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="java">        <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setPositionInfo</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">positionInfoIterator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="java">        <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setPfRead</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cachedFilter</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;">tileNum</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;">tilePosition</span><span class="o" style="font-weight: 600;">));</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">queue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">cacheFilterAndLocs</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">TileData</span> <span class="n" style="color: #333;">currentTileData</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AbstractIlluminaPositionFileReader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PositionInfo</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">locs</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Boolean</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">filterValues</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>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">FilterFileReader</span> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FilterFileReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">filterFileMap</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;">currentTileData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tileNum</span><span class="o" style="font-weight: 600;">));</span></span>

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<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Iterator</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AbstractIlluminaPositionFileReader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PositionInfo</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">positionInfoIterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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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="LC299" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="300" style="width: 35px; color: rgba(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="LC300" class="line" lang="java">        <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="301" style="width: 35px; color: rgba(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="LC301" class="line" lang="java">            <span class="n" style="color: #333;">filterValues</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">reader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="306" style="width: 35px; color: rgba(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="LC303" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">positionInfoIterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AbstractIlluminaPositionFileReader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PositionInfo</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">positions</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="java">        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">filterValue</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">filterValues</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="java">            <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AbstractIlluminaPositionFileReader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PositionInfo</span> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">positionInfoIterator</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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;">filterValue</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="java">                <span class="n" style="color: #333;">positions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">positionInfoIterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">positions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="312" style="width: 35px; color: rgba(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="LC312" class="line" lang="java">        <span class="n" style="color: #333;">cachedFilter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">currentTileData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tileNum</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">filterValues</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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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="LC311" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">cacheTile</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">TileData</span> <span class="n" style="color: #333;">tileData</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 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="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">cacheTile</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">TileData</span> <span class="n" style="color: #333;">tileData</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kd" style="font-weight: 600;"><span class="idiff">final</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">CycleData</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">currentCycleData</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 class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">tileByteArray</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">tileData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">compressedBlockSize</span><span class="o" style="font-weight: 600;">];</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// Read the whole compressed block into a buffer, then sanity check the length</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -329,11 +333,38 @@ public class CbclReader extends BaseBclReader implements CloseableIterator<CbclD</td>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">decompressedByteArray</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decompressTile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tileData</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">byteInputStream</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>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// Read uncompressed data from the buffer and expand each nibble into a full byte for ease of use</span></span>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="java">        <span class="n" style="color: #333;">cachedTile</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">promoteNibblesToBytes</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">decompressedByteArray</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="java">        <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">unNibbledByteArray</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">promoteNibblesToBytes</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">decompressedByteArray</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="java">        <span class="n" style="color: #333;">cachedTile</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filterNonPfReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tileData</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">currentCycleData</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">unNibbledByteArray</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="java">        <span class="n" style="color: #333;">cachedTilePosition</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">totalCycleCount</span><span class="o" style="font-weight: 600;">]</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="LC340" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">filterNonPfReads</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">TileData</span> <span class="n" style="color: #333;">tileData</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">CycleData</span> <span class="n" style="color: #333;">currentCycleData</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">unNibbledByteArray</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// Write buffer contents to cached tile array</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// if nonPF reads are included we need to strip them out</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC345" 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;">currentCycleData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">pfExcluded</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="java">            <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Boolean</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">filterDatas</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cachedFilter</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;">tileData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tileNum</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="java">            <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">filterDatas</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="java">                <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="java">            <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">filteredByteArray</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">filterIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="java">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">basecallIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="java">            <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">filterData</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">filterDatas</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC355" class="line" lang="java">                <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="n" style="color: #333;">readByte</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unNibbledByteArray</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">filterIndex</span><span class="o" style="font-weight: 600;">];</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC356" 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;">filterData</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="java">                    <span class="n" style="color: #333;">filteredByteArray</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">basecallIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readByte</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="java">                    <span class="n" style="color: #333;">basecallIndex</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="java">                <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="java">                <span class="n" style="color: #333;">filterIndex</span><span class="o" style="font-weight: 600;">++;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">filteredByteArray</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">unNibbledByteArray</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">promoteNibblesToBytes</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">decompressedByteArray</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">//we are going to explode the nibbles in to bytes to make PF filtering easier</span></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">unNibbledByteArray</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">decompressedByteArray</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -376,6 +407,10 @@ public class CbclReader extends BaseBclReader implements CloseableIterator<CbclD</td>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">decompressedByteArray</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">CycleData</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">getCycleData</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

411

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cycleData</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getHeaderSize</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="415" style="width: 35px; color: rgba(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="LC415" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">headerSize</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="416" style="width: 35px; color: rgba(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="LC416" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<br>

</li>

<li id="2251ea850ba98345bce132efaf72cb3836941ddb">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#2251ea850ba98345bce132efaf72cb3836941ddb"><strong>src/main/java/picard/sam/markduplicates/UmiUtil.java</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,34 +82,49 @@ class UmiUtil {</td>

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

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

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">PicardException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Duplex UMIs must be of the form X-Y where X and Y are equal length UMIs, for example AT-GA.  Found UMI, "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">umi</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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83

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC85" 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;">isTopStrand</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

<pre style="margin: 0;">-<span id="LC86" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</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 class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">DUPLEX_UMI_DELIMITER</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

<pre style="margin: 0;">-<span id="LC87" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

<pre style="margin: 0;">-<span id="LC88" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</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 class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">DUPLEX_UMI_DELIMITER</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC85" class="line" lang="java">        <span class="k" style="font-weight: 600;">switch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">getStrand</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java">            <span class="k" style="font-weight: 600;">case</span> <span class="nl">BOTTOM:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="java">                <span class="k" style="font-weight: 600;">return</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 class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">DUPLEX_UMI_DELIMITER</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC88" class="line" lang="java">                <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC89" class="line" lang="java">                    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">umi</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC91" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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

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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="LC92" class="line" lang="java"></span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC93" class="line" lang="java">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * Determines if the read represented by a SAM record belongs to the top or bottom strand.</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * Determines if the read represented by a SAM record belongs to the top or bottom strand</span></span>

</pre>

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

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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">

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * or if it cannot determine strand position due to one of the reads being unmapped.</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * Top strand is defined as having a read 1 unclipped 5' coordinate</span></span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC97" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * less than the read 2 unclipped 5' coordinate.  If a read is unmapped</span></span>

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * <span class="idiff left right">it is considered to have an unclipped 5' coordinate of 0.  If the mate</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * belongs to a different contig from the read, then the reference</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * <span class="idiff left right">we do not attempt to determine the strand to which the read or its mate belongs.</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * <span class="idiff left right">If the mate </span>belongs to a different contig from the read, then the reference</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * index for the read and its mate is used in leu of the unclipped 5' coordinate.</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param rec Record to determine top or bottom strand</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @return Top or bottom strand, <span class="idiff left right">true (top), false (bottom)</span>.</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @return Top or bottom strand, <span class="idiff left right">unknown if it cannot be determined</span>.</span></span>

</pre>

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

101

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

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

102

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

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java">    <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;">isTopStrand</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">SAMRecord</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

</td>

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

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java">    <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">ReadStrand</span> <span class="nf" style="color: #900; font-weight: 600;">getStrand</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">SAMRecord</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC105" 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;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getReadUnmappedFlag</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMateUnmappedFlag</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ReadStrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">UNKNOWN</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// If the read pair are aligned to different contigs we use</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// the reference index to determine relative 5' coordinate ordering.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// Both the read and its mate should not have their unmapped flag set to true.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC112" 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;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getReferenceIndex</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="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMateReferenceIndex</span><span class="o" style="font-weight: 600;">()))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFirstOfPairFlag</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getReferenceIndex</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMateReferenceIndex</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC113" 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;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFirstOfPairFlag</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getReferenceIndex</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMateReferenceIndex</span><span class="o" style="font-weight: 600;">()))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ReadStrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">TOP</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

116

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ReadStrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BOTTOM</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

108

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

118

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

109

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

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="java"></span>

</pre>

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

110

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

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">read5PrimeStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getReadNegativeStrandFlag</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getUnclippedEnd</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getUnclippedStart</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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

111

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

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mate5PrimeStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMateNegativeStrandFlag</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">SAMUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMateUnclippedEnd</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">SAMUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMateUnclippedStart</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

112

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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC112" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFirstOfPairFlag</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read5PrimeStart</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mate5PrimeStart</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getFirstOfPairFlag</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">read5PrimeStart</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">mate5PrimeStart</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ReadStrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">TOP</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ReadStrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BOTTOM</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num 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">

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

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -133,7 +148,22 @@ class UmiUtil {</td>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java">        <span class="n" style="color: #333;">molecularIdentifier</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">assignedUmi</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC150" 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;">duplexUmis</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java">            <span class="n" style="color: #333;">molecularIdentifier</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isTopStrand</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">TOP_STRAND_DUPLEX</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">BOTTOM_STRAND_DUPLEX</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">// Reads whose strand position can be determined will have their</span></span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">// molecularIdentifier set to include an identifier appended that</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="java">            <span class="c1" style="color: #998; font-style: italic;">// indicates top or bottom strand.</span></span>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="java">            <span class="n" style="color: #333;">ReadStrand</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getStrand</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="java">            <span class="k" style="font-weight: 600;">switch</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="java">                <span class="k" style="font-weight: 600;">case</span> <span class="nl">TOP:</span></span>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java">                    <span class="n" style="color: #333;">molecularIdentifier</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">TOP_STRAND_DUPLEX</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="java">                    <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java">                <span class="k" style="font-weight: 600;">case</span> <span class="nl">BOTTOM:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java">                    <span class="n" style="color: #333;">molecularIdentifier</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">BOTTOM_STRAND_DUPLEX</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="java">                    <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="java">                <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java">                    <span class="c1" style="color: #998; font-style: italic;">// If we can't determine strand position nothing</span></span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java">                    <span class="c1" style="color: #998; font-style: italic;">// is appended to the molecularIdentifier.</span></span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="java">                    <span class="k" style="font-weight: 600;">break</span><span class="o" style="font-weight: 600;">;</span></span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="java">        <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setAttribute</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">molecularIdentifierTag</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">molecularIdentifier</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">toString</span><span class="o" style="font-weight: 600;">());</span></span>

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<pre style="margin: 0;"> <span id="LC169" 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="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -146,4 +176,14 @@ class UmiUtil {</td>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="java">    <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;">getUmiLength</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">umi</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">umi</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="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">StringUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">countMatches</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">umi</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">DUPLEX_UMI_DELIMITER</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"></span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * An enum to hold the strand position (TOP or BOTTOM) of a read.</span></span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ReadStrand</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java">        <span class="n" style="color: #333;">TOP</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="java">        <span class="n" style="color: #333;">BOTTOM</span><span class="o" style="font-weight: 600;">,</span></span>

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="java">        <span class="n" style="color: #333;">UNKNOWN</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>

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<li id="dc629c42db1f7d3a87978e3c165dbd25e8d1cd12">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#dc629c42db1f7d3a87978e3c165dbd25e8d1cd12"><strong>src/main/java/picard/sam/markduplicates/util/OpticalDuplicateFinder.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,7 +126,7 @@ public class OpticalDuplicateFinder extends ReadNameParser implements Serializab</td>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// If there is only one or zero reads passed in (so there are obviously no optical duplicates),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// or if there are too many reads (so we don't want to try to run this expensive n^2 algorithm),</span></span>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// then just return an array of all false</span></span>

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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC129" 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;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxDuplicateSetSize</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java">        <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">readNameRegex</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff">null</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxDuplicateSetSize</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">opticalDuplicateFlags</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC131" 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="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="java"></span>

</pre>

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</li>

<li id="7b8c8bdd576e9d3a0df135db87180469ffbaea30">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#7b8c8bdd576e9d3a0df135db87180469ffbaea30"><strong>src/main/java/picard/sam/util/ReadNameParser.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ public class ReadNameParser implements Serializable {</td>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="java"></span>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">useOptimizedDefaultParsing</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// was the regex default?</span></span>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java">    <span class="kd" style="font-weight: 600;">pr<span class="idiff left right">ivate</span></span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">readNameRegex</span><span class="o" style="font-weight: 600;">;</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="java">    <span class="kd" style="font-weight: 600;">pr<span class="idiff left right">otected</span></span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">readNameRegex</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="java"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">Pattern</span> <span class="n" style="color: #333;">readNamePattern</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); 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="63" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -63,7 +63,7 @@ public class ReadNameParser implements Serializable {</td>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * @param log the log to which to write messages.</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     */</span></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="nf" style="color: #900; font-weight: 600;">ReadNameParser</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">readNameRegex</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Log</span> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="java">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">useOptimizedDefaultParsing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">readNameRegex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">DEFAULT_READ_NAME_REGEX</span></span><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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">useOptimizedDefaultParsing</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">DEFAULT_READ_NAME_REGEX</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">readNameRegex</span></span><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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">readNameRegex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readNameRegex</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;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">log</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log</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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<br>

</li>

<li id="813710362f32b1c12d752ba7601a00d9dcbdbd1d">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#813710362f32b1c12d752ba7601a00d9dcbdbd1d"><strong>src/main/java/picard/util/ThreadPoolExecutorWithExceptions.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;">picard</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">util</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;">htsjdk.samtools.util.Log</span><span class="o" style="font-weight: 600;">;</span></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;">picard.PicardException</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>

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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.util.concurrent.CancellationException</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="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +14,8 @@ import java.util.concurrent.TimeUnit;</td>

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

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC16" 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;">ThreadPoolExecutorWithExceptions</span> <span class="kd" style="font-weight: 600;">extends</span> <span class="n" style="color: #333;">ThreadPoolExecutor</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Log</span> <span class="n" style="color: #333;">log</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Log</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getInstance</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ThreadPoolExecutorWithExceptions</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">class</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Throwable</span> <span class="n" style="color: #333;">exception</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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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="java"></span>

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

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     * Creates a fixed size thread pool executor that will rethrow exceptions from submitted jobs.</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">     *</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,6 +42,7 @@ public class ThreadPoolExecutorWithExceptions extends ThreadPoolExecutor {</td>

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<pre style="margin: 0;"> <span id="LC42" 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="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(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="44" style="width: 35px; color: rgba(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="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;">t</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="o" style="font-weight: 600;">{</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="java">            <span class="n" style="color: #333;">exception</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">PicardException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMessage</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,8 +51,7 @@ public class ThreadPoolExecutorWithExceptions extends ThreadPoolExecutor {</td>

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<td class="diff-line-num 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">

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

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java">    <span class="kd" style="font-weight: 600;">protected</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">beforeExecute</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Thread</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Runnable</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java">        <span class="kd" style="font-weight: 600;">super</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">beforeExecute</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java">        <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setUncaughtExceptionHandler</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">t1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">error</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCause</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java">            <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">PicardException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Uncaught exception in thread: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getName</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" : "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCause</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">getMessage</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getCause</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="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">PicardException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Uncaught exception in thread: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t1</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getName</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" : "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMessage</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java">        <span class="o" style="font-weight: 600;">});</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>

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<br>

</li>

<li id="12247ce6b4d138b1a549e9a057275fa85001fab8">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#12247ce6b4d138b1a549e9a057275fa85001fab8"><strong>src/test/java/picard/analysis/CollectRnaSeqMetricsTest.java</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -382,6 +382,59 @@ public class CollectRnaSeqMetricsTest extends CommandLineProgramTest {</td>

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">metrics</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PCT_R2_TRANSCRIPT_STRAND_READS</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.333333</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="java">    <span class="nd">@Test</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC386" 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;">testPctRibosomalBases</span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"chr1"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">ignoredSequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"chrM"</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

389

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

390

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// Create some alignments that hit the ribosomal sequence, various parts of the gene, and intergenic.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

391

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">SAMRecordSetBuilder</span> <span class="n" style="color: #333;">builder</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMRecordSetBuilder</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">SAMFileHeader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">SortOrder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">coordinate</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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

392

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// Set seed so that strandedness is consistent among runs.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

393

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="java">        <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setRandomSeed</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

394

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sequenceIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeader</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">getSequenceIndex</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

395

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

396

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="java">        <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addPair</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"rrnaPair"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sequenceIndex</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">400</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">500</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"35I1M"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"35I1M"</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

397

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="java">        <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addFrag</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"frag1"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sequenceIndex</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">150</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"34I2M"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"*"</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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

398

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="java">        <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addFrag</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"frag2"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sequenceIndex</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">190</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"35I1M"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"*"</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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

399

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="java">        <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addFrag</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ignoredFrag"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeader</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">getSequenceIndex</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ignoredSequence</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;">false</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

400

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">samFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createTempFile</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tmp.collectRnaSeqMetrics."</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">".sam"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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

401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="java">        <span class="n" style="color: #333;">samFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">deleteOnExit</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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

402

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="java">        <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">SAMFileWriter</span> <span class="n" style="color: #333;">samWriter</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMFileWriterFactory</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">makeSAMWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeader</span><span class="o" style="font-weight: 600;">(),</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">samFile</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="java">            <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">SAMRecord</span> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getRecords</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="java">                <span class="n" style="color: #333;">samWriter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addAlignment</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

405

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

406

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// Create an interval list with one ribosomal interval.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Interval</span> <span class="n" style="color: #333;">rRnaInterval</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">300</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">520</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"rRNA"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">IntervalList</span> <span class="n" style="color: #333;">rRnaIntervalList</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">IntervalList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">builder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getHeader</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="java">        <span class="n" style="color: #333;">rRnaIntervalList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rRnaInterval</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">rRnaIntervalsFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createTempFile</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tmp.rRna."</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">".interval_list"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="java">        <span class="n" style="color: #333;">rRnaIntervalsFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">deleteOnExit</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="java">        <span class="n" style="color: #333;">rRnaIntervalList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rRnaIntervalsFile</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// Generate the metrics.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">File</span> <span class="n" style="color: #333;">metricsFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">File</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">createTempFile</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"tmp."</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">".rna_metrics"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

418

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="java">        <span class="n" style="color: #333;">metricsFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">deleteOnExit</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

419

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

420

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</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="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[]{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

421

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="java">                <span class="s" style="color: #d14;">"INPUT="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">samFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAbsolutePath</span><span class="o" style="font-weight: 600;">(),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

422

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="java">                <span class="s" style="color: #d14;">"OUTPUT="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">metricsFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAbsolutePath</span><span class="o" style="font-weight: 600;">(),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

423

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="java">                <span class="s" style="color: #d14;">"REF_FLAT="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">getRefFlatFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">getAbsolutePath</span><span class="o" style="font-weight: 600;">(),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

424

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="java">                <span class="s" style="color: #d14;">"RIBOSOMAL_INTERVALS="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rRnaIntervalsFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getAbsolutePath</span><span class="o" style="font-weight: 600;">(),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

425

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="java">                <span class="s" style="color: #d14;">"STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND"</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

426

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="java">                <span class="s" style="color: #d14;">"IGNORE_SEQUENCE="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ignoredSequence</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

427

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="java">        <span class="o" style="font-weight: 600;">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">runPicardCommandLine</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">MetricsFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RnaSeqMetrics</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Comparable</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="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MetricsFile</span><span class="o" style="font-weight: 600;"><>();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

431

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="java">        <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">read</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FileReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">metricsFile</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

432

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

433

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">RnaSeqMetrics</span> <span class="n" style="color: #333;">metrics</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="na" style="color: teal;">getMetrics</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

434

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">metrics</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PCT_RIBOSOMAL_BASES</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.4</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="java"></span>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">File</span> <span class="nf" style="color: #900; font-weight: 600;">getRefFlatFile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="386" style="width: 35px; color: rgba(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="LC439" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// Create a refFlat file with a single gene containing two exons, one of which is overlapped by the</span></span>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="java">        <span class="c1" style="color: #998; font-style: italic;">// ribosomal interval.</span></span>

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<br>

</li>

<li id="4a3455d3b3da89fba102450e92ca3771afab474e">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#4a3455d3b3da89fba102450e92ca3771afab474e"><strong>src/test/java/picard/illumina/CollectIlluminaBasecallingMetricsTest.java</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,20 +157,20 @@ public class CollectIlluminaBasecallingMetricsTest {</td>

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<pre style="margin: 0;"> <span id="LC157" 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;">testNovaseqIndexedRun</span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="n" style="color: #333;">Exception</span> <span class="o" style="font-weight: 600;">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">MetricsFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">IlluminaBasecallingMetrics</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="n" style="color: #333;">metricsFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runIt</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="s" style="color: #d14;">"151T8B8B151T"</span><span class="o" style="font-weight: 600;">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="java">                <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">File</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls"</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="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new_line old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">IlluminaBasecallingMetrics</span> <span class="n" style="color: #333;">laneMetric</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metricsFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMetrics</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;"><span class="idiff left">metricsFile</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">getMetrics</span></span><span class="o" style="font-weight: 600;"><span class="idiff">().</span></span><span class="na" style="color: teal;"><span class="idiff">size</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">IlluminaBasecallingMetrics</span> <span class="n" style="color: #333;">laneMetric</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metricsFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMetrics</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="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">LANE</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"1"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assert<span class="idiff left">Null</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">laneMetric</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">MOLECULAR_BARCODE_SEQUENCE_1</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assert<span class="idiff left">Null</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">laneMetric</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff right">MOLECULAR_BARCODE_NAME</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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164

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<td class="diff-line-num new_line old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC164" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MEAN_CLUSTERS_PER_TILE</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;"><span class="idiff left right">28</span>.0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

162

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assert<span class="idiff left">Equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">laneMetric</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">MOLECULAR_BARCODE_SEQUENCE_1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"CACCTAGTACTCGAGT"</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

163

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assert<span class="idiff left">Equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">laneMetric</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">MOLECULAR_BARCODE_NAME</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"SA_CACCTAGTACTCGAGT"</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

164

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MEAN_CLUSTERS_PER_TILE</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;"><span class="idiff left right">1</span>.0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

165

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<td class="diff-line-num new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

165

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">SD_CLUSTERS_PER_TILE</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

166

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<td class="diff-line-num new_line old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MEAN_PF_CLUSTERS_PER_TILE</span><span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;"><span class="idiff left right">25</span>.0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

166

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MEAN_PF_CLUSTERS_PER_TILE</span><span class="o" style="font-weight: 600;">,</span><span class="mf" style="color: #099;"><span class="idiff left right">1</span>.0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

167

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<td class="diff-line-num new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

167

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">SD_PF_CLUSTERS_PER_TILE</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

168

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<td class="diff-line-num new_line old" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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="LC168" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MEAN_PCT_PF_CLUSTERS_PER_TILE</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;"><span class="idiff left right">89.29</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

168

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">MEAN_PCT_PF_CLUSTERS_PER_TILE</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;"><span class="idiff left right">100.0</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

169

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<td class="diff-line-num new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

169

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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="LC169" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">SD_PCT_PF_CLUSTERS_PER_TILE</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

170

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<td class="diff-line-num new_line old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">TOTAL_BASES</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">1691</span>2</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

171

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<td class="diff-line-num new_line old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">TOTAL_READS</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">11</span>2</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PF_BASES</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">15100</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PF_READS</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">100</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">TOTAL_BASES</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">30</span>2</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">TOTAL_READS</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>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PF_BASES</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">302</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">laneMetric</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">PF_READS</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">metricsFile</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMetrics</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">size</span><span class="o" style="font-weight: 600;">(),</span><span class="mi" style="color: #099;">6</span><span class="o" style="font-weight: 600;">);</span></span>

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<br>

</li>

<li id="e1b7610ac081822bc869b241576e7cb24565e95a">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#e1b7610ac081822bc869b241576e7cb24565e95a"><strong>src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -288,8 +288,8 @@ public class ExtractIlluminaBarcodesTest extends CommandLineProgramTest {</td>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">runPicardCommandLine</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="289" style="width: 35px; color: rgba(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="289" style="width: 35px; color: rgba(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="LC289" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">MetricsFile</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ExtractIlluminaBarcodes</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BarcodeMetric</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="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">MetricsFile</span><span class="o" style="font-weight: 600;"><>();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="290" style="width: 35px; color: rgba(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="LC290" class="line" lang="java">        <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">read</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FileReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">metricsFile</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMetrics</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">P<span class="idiff left right">F_P</span>ERFECT_MATCHES</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="s" style="color: #d14;">"Got wrong number of perfect matches"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMetrics</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;"><span class="idiff left right">PF_</span>ONE_MISMATCH_MATCHES</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Got wrong number of one-mismatch matches"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMetrics</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">PERFECT_MATCHES</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="s" style="color: #d14;">"Got wrong number of perfect matches"</span><span class="o" style="font-weight: 600;">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getMetrics</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: teal;">ONE_MISMATCH_MATCHES</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Got wrong number of one-mismatch matches"</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="java">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

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<br>

</li>

<li id="916509529fd4b66c5557838d020d201d6b9921b7">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#916509529fd4b66c5557838d020d201d6b9921b7"><strong>src/test/java/picard/illumina/parser/FilterParserTest.java</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,7 +94,7 @@ public class FilterParserTest {</td>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="java"></span>

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

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java">        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">expectedValue</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="java">            <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">());</span></span>

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java">            <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">isPf<span class="idiff left right">Read</span></span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">expectedValue</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="java">            <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">isPf</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">expectedValue</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC99" class="line" lang="java"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertFalse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</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="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,7 +103,7 @@ public class FilterParserTest {</td>

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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;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">seekToTile</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]);</span></span>

</pre>

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

104

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104

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java">        <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">expectedValue</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

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

105

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105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="java">            <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

106

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java">            <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">isPf<span class="idiff left right">Read</span></span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">expectedValue</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java">            <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">isPf</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">expectedValue</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java"></span>

</pre>

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

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109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertFalse</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,7 +137,7 @@ public class FilterParserTest {</td>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="java">            <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="java">            <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertTrue</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">hasNext</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<td class="diff-line-num new_line old" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC140" class="line" lang="java">            <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">isPf<span class="idiff left right">Read</span></span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">expectedValue</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">" Failed on read: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java">            <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">next</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">isPf</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">expectedValue</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">" Failed on read: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="java">            <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(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="142" style="width: 35px; color: rgba(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="LC142" class="line" lang="java">        <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="java"></span>

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<li id="47042314502a41f6758d5d534f7b8f4d1e996450">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#47042314502a41f6758d5d534f7b8f4d1e996450"><strong>src/test/java/picard/sam/markduplicates/AbstractMarkDuplicatesCommandLineProgramTest.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">@@ -652,6 +652,17 @@ public abstract class AbstractMarkDuplicatesCommandLineProgramTest {</td>

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652

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="java">        <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">runTest</span><span class="o" style="font-weight: 600;">();</span></span>

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653

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653

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

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654

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654

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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="LC654" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

655

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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="LC655" class="line" lang="java">    <span class="nd">@Test</span></span>

</pre>

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656

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<pre style="margin: 0;">+<span id="LC656" 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;">testOpticalDuplicateBehaviorNullRegex</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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657

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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="LC657" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">AbstractMarkDuplicatesCommandLineProgramTester</span> <span class="n" style="color: #333;">tester</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getTester</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

658

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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="LC658" class="line" lang="java">        <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSamRecordSetBuilder</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: teal;">setReadLength</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">68</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

659

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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="LC659" class="line" lang="java">        <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setExpectedOpticalDuplicate</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

660

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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="LC660" class="line" lang="java">        <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addMatePair</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"RUNID:1:1:15993:13361"</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="mi" style="color: #099;">41212324</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">41212310</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"33S35M"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"19S49M"</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_BASE_QUALITY</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

661

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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="LC661" class="line" lang="java">        <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addMatePair</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"RUNID:1:1:16020:13352"</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="mi" style="color: #099;">41212324</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">41212319</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"33S35M"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"28S40M"</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">DEFAULT_BASE_QUALITY</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

662

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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="LC662" class="line" lang="java">        <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"READ_NAME_REGEX=null"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

663

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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="LC663" class="line" lang="java">        <span class="n" style="color: #333;">tester</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">runTest</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

664

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

665

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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="LC665" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC666" class="line" lang="java">    <span class="nd">@DataProvider</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"secondarySupplementaryData"</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="java">    <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Object</span><span class="o" style="font-weight: 600;">[][]</span> <span class="nf" style="color: #900; font-weight: 600;">secondarySupplementaryData</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="java">        <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Object</span><span class="o" style="font-weight: 600;">[][]</span> <span class="o" style="font-weight: 600;">{</span></span>

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<br>

</li>

<li id="754eaac80aeed7cf98a70fd23c33ca436613b0cc">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#754eaac80aeed7cf98a70fd23c33ca436613b0cc"><strong>src/test/java/picard/sam/markduplicates/UmiUtilTest.java</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,44 +39,51 @@ public class UmiUtilTest {</td>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java">    <span class="kd" style="font-weight: 600;">private</span> <span class="n" style="color: #333;">Object</span><span class="o" style="font-weight: 600;">[][]</span> <span class="nf" style="color: #900; font-weight: 600;">testIsTopStrandDataProvider</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">read1</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="LC41" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">read2</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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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ReadStrand</span> <span class="n" style="color: #333;">top</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ReadStrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">TOP</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ReadStrand</span> <span class="n" style="color: #333;">bottom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ReadStrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">BOTTOM</span><span class="o" style="font-weight: 600;">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ReadStrand</span> <span class="n" style="color: #333;">unknown</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ReadStrand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">UNKNOWN</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;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Object</span><span class="o" style="font-weight: 600;">[][]{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1R2 pair, reads point inwards, top strand</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F1R2 pair, reads point inwards, top strand</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1R2 pair, reads point outwards</span></span>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

46

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F1R2 pair, reads point outwards</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F2R1 pair</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F2R1 pair</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

49

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1F2 pair</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

50

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F1F2 pair</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

51

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>     <span class="c1" style="color: #998; font-style: italic;">// Read 1 in R1R2 pair</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

52

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>     <span class="c1" style="color: #998; font-style: italic;">// Read 2 in R1R2 pair</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1R2 chimera</span></span>

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F1R2 chimera</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

55

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F2R1 chimera</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">},</span>  <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F2R1 chimera</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F2R1 chimera</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

46

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1R2 pair, reads point inwards, top strand</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F1R2 pair, reads point inwards, top strand</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bottom</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1R2 pair, reads point outwards</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bottom</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F1R2 pair, reads point outwards</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F2R1 pair</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F2R1 pair</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1F2 pair</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F1F2 pair</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>     <span class="c1" style="color: #998; font-style: italic;">// Read 1 in R1R2 pair</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="java">                <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="mi" style="color: #099;">200</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="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>     <span class="c1" style="color: #998; font-style: italic;">// Read 2 in R1R2 pair</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1R2 chimera</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bottom</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F1R2 chimera</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">top</span><span class="o" style="font-weight: 600;">},</span>    <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F2R1 chimera</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bottom</span><span class="o" style="font-weight: 600;">},</span>  <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F2R1 chimera</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read2</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">bottom</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 2 in F2R1 chimera</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">unknown</span><span class="o" style="font-weight: 600;">},</span>   <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1R2 pair, top strand, read not mapped</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">unknown</span><span class="o" style="font-weight: 600;">},</span>  <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1R2 pair, top strand, mate not mapped</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="java">                <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="mi" style="color: #099;">100</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="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">unknown</span><span class="o" style="font-weight: 600;">},</span>  <span class="c1" style="color: #998; font-style: italic;">// Read 1 in F1R2 pair, top strand, neither mapped</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java">        <span class="o" style="font-weight: 600;">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(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="65" style="width: 35px; color: rgba(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="LC65" class="line" lang="java">    <span class="o" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(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="66" style="width: 35px; color: rgba(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="LC66" class="line" lang="java"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java">    <span class="nd">@Test</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">dataProvider</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"topStrandDataProvider"</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="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;">testIsTopStrand</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">referenceIndex</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignmentStart</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mateReferenceIndex</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mateAlignmentStart</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java">                                <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">firstOfPairFlag</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">negativeStrandFlag</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">mateNegativeStrandFlag</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java">                                <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">topStrand</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java">                                <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">mapped</span><span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">mateMapped</span><span class="o" style="font-weight: 600;">,</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java">                                <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">ReadStrand</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(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="LC73" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">readLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java">        <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">contigLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">500</span><span class="o" style="font-weight: 600;">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java">        <span class="n" style="color: #333;">SAMFileHeader</span> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMFileHeader</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java">        <span class="n" style="color: #333;">SAMSequenceDictionary</span> <span class="n" style="color: #333;">sequenceDictionary</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMSequenceDictionary</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java">        <span class="kd" style="font-weight: 600;"><span class="idiff left">final</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">SAMFileHeader</span> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMFileHeader</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC76" class="line" lang="java">        <span class="kd" style="font-weight: 600;"><span class="idiff left">final</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">SAMSequenceDictionary</span> <span class="n" style="color: #333;">sequenceDictionary</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMSequenceDictionary</span><span class="o" style="font-weight: 600;">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

70

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<td class="diff-line-num new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

77

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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="LC77" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

71

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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

78

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="java">        <span class="n" style="color: #333;">sequenceDictionary</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addSequence</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMSequenceRecord</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"chr1"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">contigLength</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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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="LC79" class="line" lang="java">        <span class="n" style="color: #333;">sequenceDictionary</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">addSequence</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMSequenceRecord</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"chr2"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">contigLength</span><span class="o" style="font-weight: 600;">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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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="LC80" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

74

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC74" 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;">out</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="n" style="color: #333;">sequenceDictionary</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">getSequences</span><span class="o" style="font-weight: 600;">());</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

75

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

76

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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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="LC81" class="line" lang="java">        <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setSequenceDictionary</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sequenceDictionary</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

77

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

82

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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="LC82" class="line" lang="java"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

78

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<td class="diff-line-num new_line old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC78" class="line" lang="java">        <span class="n" style="color: #333;">SAMRecord</span> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMRecord</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

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

<pre style="margin: 0;">+<span id="LC83" class="line" lang="java">        <span class="kd" style="font-weight: 600;"><span class="idiff left">final</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">SAMRecord</span> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SAMRecord</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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

84

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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="LC84" class="line" lang="java"></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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

<pre style="margin: 0;">+<span id="LC85" class="line" lang="java">        <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setReadUnmappedFlag</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">mapped</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

86

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

<pre style="margin: 0;">+<span id="LC86" class="line" lang="java">        <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setMateUnmappedFlag</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">mateMapped</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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

87

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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="LC87" class="line" lang="java">        <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setReadPairedFlag</span><span class="o" style="font-weight: 600;">(</span><span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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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="LC88" class="line" lang="java"></span>

</pre>

</td>

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

82

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<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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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="LC89" class="line" lang="java">        <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setCigarString</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">readLength</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"M"</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -92,7 +99,7 @@ public class UmiUtilTest {</td>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="java">        <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setReadNegativeStrandFlag</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">negativeStrandFlag</span><span class="o" style="font-weight: 600;">);</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="java">        <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">setMateNegativeStrandFlag</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mateNegativeStrandFlag</span><span class="o" style="font-weight: 600;">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left">isTopStrand</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rec</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">topS</span>trand</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">

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java">        <span class="n" style="color: #333;">Assert</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">assertEquals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">UmiUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;"><span class="idiff left">getStrand</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rec</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">s</span>trand</span><span class="o" style="font-weight: 600;">);</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="java">    <span class="nd">@DataProvider</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"brokenUmiProvider"</span><span class="o" style="font-weight: 600;">)</span></span>

</pre>

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<br>

</li>

<li id="3c44e3e5eb22a09e90c4c23b3232c2fdda56ac9d">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#3c44e3e5eb22a09e90c4c23b3232c2fdda56ac9d"><strong>testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz</strong></a>

<hr>

No preview for this file type

<br>

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<li id="971a7324d3259fbd2bc1abe13be49e918c57d477">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#971a7324d3259fbd2bc1abe13be49e918c57d477"><strong>testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/s_1_1102_barcode.txt.gz</strong></a>

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<li id="be3c2bcd0d53d74bb9e870efd33f725010a5708d">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#be3c2bcd0d53d74bb9e870efd33f725010a5708d"><strong>testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.1.fastq</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,10 +6,6 @@ TGATGGTTTCGGGNTTTAGACAGTGTCATGCCTATTCCNTGGTANTCTTTGTTAACCTACGCCTCATGCTCGAATTCGCG</td>

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6

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6

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

</pre>

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

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">+</span>

</pre>

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">FFF!-!-!F!!!!##!F#!FF8!FF-!#8!8F-8!----F-!-F8--88-FF!-!8F-#88#-8F!8F#88-8!!FF#!F8!8!!F!F-F-F!8F8FF!8---8-FFF8---8-8--!!-F8-!8888F8F8!F8FFF--!F!-8FFF--F</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1054:1000 1:Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">F!!!8--8#88-FF!#--FF-88-88F-!8!F-!--F8F8!FFF8-8!F8F8FF--F-!F--F-F#-8!-F-FF8888F-----F8#!F!!8F!-8F!FFF!-!!---F--88-88-F8F-F!----FFF!!8F!8FFF-#8-88-!F-88</span>

</pre>

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

13

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

9

</td>

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1072:1000 1:N:0:</span>

</pre>

</td>

</tr>

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

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

14

</td>

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

10

</td>

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

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

</pre>

</td>

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

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

15

</td>

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

11

</td>

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">+</span>

</pre>

</td>

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

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -26,10 +22,6 @@ NTCTNANATTAAGTGCGGCAGNTGGGGCCCCCTGGTTTGAGTNAAATTGTGCGTCTATCTTACGCGGANGNAATGNCAGG</td>

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

26

</td>

<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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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="LC22" class="line" lang="plaintext">TTTTCTTTGTTANGCCGTCNATGGGTCCNGGCCCACCGTACANACCCATCAGCGTCTGACGNCCGTACTTCGNTACTTATGGTGACTGTGANTGCCACGACTTGTCATNTACTTGGGGTTGTGANTANTACACCCTATCCGAACTTNAGGT</span>

</pre>

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

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

27

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

</td>

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

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

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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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="LC24" class="line" lang="plaintext">F8F-8!-!F8-8#!FFFF-#FF--F8!8#8!F-8-!!--8!-#-F-88!8-!FF!FF8F8F#F-FF8!88-8#--8!F-F8--F-!8F888#!!--8!F8888!F!8!#88-F88!!-F!F8!8#88#F-8F!-F!8!8!!8F-F8#88FF</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1145:1000 1:Y:0:</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">TTGTCNCCTTNGCTAAAGATCTCCGTCGCTCGTCTCCTGNCCCGTATCTACCTAAGCCTNCTGCGNGGTTCGTAGCCCGGCCTACAAGGCAGGCTTCANNTNTGCGGNGGGACNGAAACGCCACGCTAACCGCTCAGGCAGTAGAGCTAGT</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">!-8-F#!8--#FF8F-FF---!F!!!8-!!F88!!!--!#!8F88F!-!-F-8F-FFF!#FF!8-#!F-8!!!88F!!8!-!888F-!FF8F88-8!-##!#!!8!8#-!FF!#-F888!F-F--FFF88888F8F------FFF!!8-8!</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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

25

</td>

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

<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1163:1000 1:N:0:</span>

</pre>

</td>

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

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

34

</td>

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

26

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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="LC26" class="line" lang="plaintext">TCCTNCANTCGCACCGGAGAATTCCCACGATTCCCAAGCNAANACGATCTAATCTGAGCTTAGAACGAACAGACTCGGTAGGGGGATATTGTATCGCTGCCGTCGCGTGCTATGCTACGGTCTCNGTTATAATGGCNTTTTGGTCGCTTTA</span>

</pre>

</td>

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

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

35

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

27

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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="LC27" class="line" lang="plaintext">+</span>

</pre>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -86,10 +78,6 @@ F-!F-8!-!F88-8!##!!---F!--!-!#-#F8-8-FF--8F8!#--FFF8-F-8!-#8!88-8F-!F8-F8-F-8#!-</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

86

</td>

<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

78

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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="LC78" class="line" lang="plaintext">TACTCNGTGGACTTGTATCCNGGACTTTCTCTCTGNTACTGGGTTNCGCCGAACTCCCCGTTNAGCCATCNCGGTGCTGGACCACANATCGCGTCNGACATGCGCACTAGNCGAACCCTATACTCTANTTCNCCTTCGCTTCGGCAGTTGT</span>

</pre>

</td>

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

87

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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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="LC79" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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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="LC80" class="line" lang="plaintext">-888!#8FFF-F!-8!F!F-#!8-F888F8-8F!8#!FF!!8-!-#-8F!!8F8-F88!-F!#-!8-88!#-F8F88!F8-!F-F8#F!F!F!--#8-8-!F8!8-F-F-#FF8F-F8!-!88-!8F#!!8#88-8!F!!8F8!-F88!FF</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

89

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1452:1000 1:Y:0:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

90

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">TNGGGCGCAGTCCGGGGTTAAANCAGTTAGTCGGCGTCGCCTAACAAGCTCTTGAGCCATTGCGGCTTNTTATGATGCCTCAATTGTTGGGCCTGTGAGACCGGGGCGNGGGCCGCAAAGGCGNCNTAGTCTCNGAATTACAACCCTGNCG</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

91

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">+</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

92

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">-#FF!8!8F-8!FF8-F8!--8#F88FF-FF8888!!8!-8!-F8FFF8-!F88FF-F8-!!-!-F8F#!-8-!-F-!F!8FFF8!!8F!!-!!FFF-!F!!8!F8!F#F--!F8--888888#!#-8--!-F#-888-8!------F#8!</span>

</pre>

</td>

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

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

93

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

</td>

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

<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1470:1000 1:N:0:</span>

</pre>

</td>

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

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

94

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

82

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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="LC82" class="line" lang="plaintext">NATCTTTGGGATCATGAATTAAGGATTGTCCATGCGACAAGCNATGTACNACAGCGNACAGAATTGNTACGATGAACGTCGTAGTTGCGTTACCAAGGCACTAGNATTACCCTCTNGGCCTCGATTCGNCCACCCTCTTGGNGGTCCCGAG</span>

</pre>

</td>

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

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

95

</td>

<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

</td>

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

<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">+</span>

</pre>

</td>

</tr>

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

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,10 +98,6 @@ NGGAAANGGATAANCCAGACACCCAANGGATATGTAGCATTGTTATACCGATCCTTGCCGCTTTTTGGTAAGCAGAGGAC</td>

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

110

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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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="LC98" class="line" lang="plaintext">CAGTGTTTGTTCGAATCCGCTCCCTTCTGCTGACGTGGGTNNNNGGNAACCGAAACGCTTTTCTCCCACNCCGGNGTCGTTCAACTCTANATGGGACAGCGCATGGTTCGTCTANGCNTGACTCGTGGCANACGTCCTACGACCGCTAAAT</span>

</pre>

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

111

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

99

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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="LC99" class="line" lang="plaintext">+</span>

</pre>

</td>

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

112

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

100

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

<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">F-!8--!F-F-8!F8F888!!!F8!F-8F!!F-F-F!-!F####!!#-FF8!F-F!8FF--8F-8FF-!#!--F#FF-!8FFF---F!-#8-F!!8!--F!FF8-88FF8--88#F-#!!-FF!F---!F#8F--88!F-!--!8!8F8-8</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1054:1000 1:Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

114

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">CGGGNCCGCCAGATNTTCCCCGTTCCCACGGACGTTCCTTGGCAGCGCTACTGTCGGGGTTGATCATGCCGGTGTAGCAGGCGTNCCGGACAGTGAACTAANGTCTTGATTCCACCGNNCATAGCNTCTGATACACCTCAATTCGAGTTCA</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">--8-#-8F8FF-FF#--F8!--8--F8F!!F88F-!!F8!!8--F8F888F8F!--8!88F-F88--!F88-F!--FF-8-FF!#F!-88F-8FFFF-!-F#-F8!-!8!!-88!F-##!F-88!#F-F---FF8FF8!8F-8F-F!-8!8</span>

</pre>

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

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

117

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

101

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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="LC101" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1072:1000 1:N:0:</span>

</pre>

</td>

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

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

118

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

102

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

<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">GCGCTTGTTCCGATTTGTNTGGCGCTGCGGCAGCCTGATCGGNGCGCCTTGGTNGAGAGGCGCACTTGCACTANCGNCGGGCTACCGCCANACGTTTTCTCTGCCGGNAGCCGTATCCGGTTGGATNTTCCGNCCATCCACGAACTTCATC</span>

</pre>

</td>

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

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

119

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

103

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

<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">+</span>

</pre>

</td>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,10 +114,6 @@ TTANGGGGAGTGCNAAGGNCTTANAGTTCACCGAGCCCATAGCCTCNTGTTGTTGCGNGGGGGGTTCCTGTGCTGCCNTT</td>

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

130

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

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

<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext">GCCNAACGATCTTNTTTGCTCNNCGTGNTGCTTGGTCTTCTTGTCTCTAACTANCGTGTAGTGAGAGTNTCTCTCTCGAGCGTNTCTGGATTGCNCGACGGACGAGGAATTAGTGCTCAGTGTATCGGACCNTTTTCTGGCCGCATGCAGC</span>

</pre>

</td>

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

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

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">8!-#8-8!-F!-8#!8-!88-##8-FF#FFFFFF!!F-F-F-FF!F--8-8-8#!!!!!88-!F-F-!#8---88!FF8-FF-#-!8-!88-8!#!8--F-FF8FF88F!F8F8!!8!-F!88-!!-F8!F#!8---!-!F!--8--!F!8</span>

</pre>

</td>

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1145:1000 1:Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">AGATTTGTCAGAGTGTNTNTCAGCGGTANCGTAGTAGGCGGTGTTGGGCCGGTTCNTNTANTGNTCGAGCAAGNNACGGGCACACTGNCCATTNATCCTNATGCAAAAGCNTGGNCCCNTGGGAGGAGCCTAGCGAGCGGGGGCGTTTTTA</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">8-F-8FF88F!-!F!F#!#!-F-8F!!-#8F888-F!8!8!!8!888-!F!FF!-#F#8-#!F#F-!88-8F!##-F--!--FF-8F#!8FF8#--FF-#8F!-FFFF!8#8!F#-!-#8-FFF!8-FF!8-8--FF!-!8-!!F!!-8--</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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117

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1163:1000 1:N:0:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext">GATACGGTGTTATTCTTCTTGATTTGACTACGNGTCCGACAACNTATTCGTGGAAACACGGCCCAATAGCGCTNGCCCNACAGCTTTATAGTGTCANCAGTGATTACGTCGNTGTCAGGGTTTACAATGNAGNGCAAGCGTTTGGCGGCGA</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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

119

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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="LC119" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,10 +174,6 @@ TGACTACTTAGTAACGGNGNCCGTGGCCGCTACTGCGCCGAGGTTTTTATGTTTGNCAACTGGAAGGAGGCAATAAACTA</td>

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<td class="diff-line-num old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(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="LC174" class="line" lang="plaintext">CGGGGACAGTGTCATTATCGCCNCCGNGCAGGNTTAAGNCNTNCCGGNGGGGGCAGTGCTATTCCGATGTCCCCGNAATAGTCNTGGGTCAGTACCCATGCCCCTTATANAGCNATATNGTAGNCAGCGGCTTGCGGCTCAGCCCATTTTA</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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175

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext">-8-8---F!8!-8-!!FF8!!-#8!-#8F-F8#F--8F#-#8#FF8F#-8FFF8-!8-!-8FF!-!-88F88!-!#8F8F-FF#!!-F888-F-!-888!FF!8FF8F-#88!#888!#8FF8#!888!-88!!8--8!!-8-FF-88!8F</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1452:1000 1:Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext">GTTCCGGACGAAGGACTGGATTGCTGCTCAGAGATCCCGGTTCCAGGGTCGGTNCAATTTGTCCGCCAGGTGGANCTTGTTCTTTCAGACTAAGGTTNNAGTGANGCCAGCATTAAGATACAGAAACAACTCGTCCCCTNTCTGACGATCA</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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="LC199" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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="LC200" class="line" lang="plaintext">8-FF8!---FF8!!8!-F!8F!8--FF-8F!F!F!!!F-!8F!-8F8F!8!88#FF-88FF!-!-8!F8-!!--#!!-FFF-F8F8--8-F--8!-!##-F!8F#-88F8F-!F-F8F!8-8-FFF8FF-8F-!88!8!#-8F8-8F---F</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="LC177" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1470:1000 1:N:0:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext">CAGACCGCGGCTCTGGATCACCTCCGACGGGTAGTGACANCTACCTNAATCCGTCCAAGCAATGTGCAGTTCTTAATGACTTGGCTCGAGTAGTCCTGACCAANGAACGGACGTTCTTCGANGATAGGTGGGAGNTGGCTTCACGCTTTAC</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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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="LC179" class="line" lang="plaintext">+</span>

</pre>

</td>

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<br>

</li>

<li id="b5aec946ccfb0c854b9094ba2bccab5bd883a645">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#b5aec946ccfb0c854b9094ba2bccab5bd883a645"><strong>testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.2.fastq</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,10 +6,6 @@ F-!F8--8F#F#88#-#-FF##F-8!-8#88-F-F-F8F-F-F8F#-8!--8F8-!F!8F!--8-8!FFFFF8F!FFF-F</td>

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

6

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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

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

</pre>

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

7

</td>

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

7

</td>

<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="plaintext">+</span>

</pre>

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<td class="diff-line-num 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">

8

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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">

8

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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="LC8" class="line" lang="plaintext">FF!8F#F88F-!F88--FF----8-F88FF8#!88-!F#-FF-8FF--88!F!FF8FF!8-F--8-!88888#!-8!#F#88F888-!--F--888F-8F-FF8F8---88!F!-FF!-!--FF--F88!-!-!FF!#!88F-88F-#88F</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1054:1000 2:Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

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

</pre>

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

11

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">-F#8!8#-F8---!F8888-8F-F---F888#!FF!F!--!!8FF8F8!F8FF!8--###F!F-!8!-F8F!-F--F!8!8F#88!--#!--8!-8--8-F8-8#!8---F8-88#!-FFFF#--F--!-!-!F#8!#F8F---8FFFFFF</span>

</pre>

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

13

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

9

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1072:1000 2:N:0:</span>

</pre>

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

14

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

10

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

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

</pre>

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

15

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

11

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">+</span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -26,10 +22,6 @@ TGTGTGNACTATCAATCGACCAGTACTTAGTTCAGCACCGCCCTACTCGGCACTGCTAGCGGGTCGACCTGGATAGCCGT</td>

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

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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

</pre>

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

27

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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

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

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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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="LC24" class="line" lang="plaintext">F!888-FF!!!#--!F-F!F!88-F8!!!!-!---!8!F8#-8F!F-!FF!F-8-8#88F8-FFFFF-!--!#8F!F!-8F!F-F88F8#8#F88888--8-88!!F-8FF8-F!F!FFF-F-F888--8FFFFF--88-8-8--!FFF--</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1145:1000 2:Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">TCACTCTTCATTNTGGTCTTGCTGAATCAGCTTATCTTGATGAGAGCGNCTCCTGACTGGGAGGNTGCCCNCCAGANTATNTGACCCCGNGACAGCTGTGACNATCAGGAGCCNNTTCCGCTCCCCCGNAGTCATGTATCGCTTTAAAGAT</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">!F8-F-8!F8-8#!!FF-!888F8888-888!F8!--8!FFF-F888-#8!!!-88-!-!!F!F#8F8!F#-F-!8#!8-#F8-!!8!-#F8---F8FFFFF#-F-F-F-8-!##--8!-F!!88FF8#88FF8-88F!888!!8-F8-88</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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

25

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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="LC25" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1163:1000 2:N:0:</span>

</pre>

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

34

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

26

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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="LC26" class="line" lang="plaintext">GGNGCGCNCTCCGCACGCCANTAGCANCTTGNGTAGGCCCTTNTTTCCAGTTTCTGGTAGGTCTCGAGGCGTATCGTTTNCGGCGTCTTTCCACTGAAAGGGGGTCTTAGGATGGTATCTGGTNGCGNACGTGAGTGTATCGCACGTACCC</span>

</pre>

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

35

</td>

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

27

</td>

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

<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">+</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -86,10 +78,6 @@ TGGTCCTCTGGTCAGCAGTTCTAAGTGCCGTCTATGGNTGGGTNCACCANCGCTANGTNATAGGTCCCTAGGTCGGGCGT</td>

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

<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

86

</td>

<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

78

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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="LC78" class="line" lang="plaintext">TTTGTTTCAGGGCCTTTGCCGTNCGCANTATTGTGTCTCTTCCCAGCAGCTGTCCTTAATGATNTAGCAGATCGCCTGTGCATTANCGCACCTCNTCGTANAGGGGTGTTCCAACGCATACANCTGCNTGGNCGTNNCAATGAATCAGATT</span>

</pre>

</td>

</tr>

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

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

87

</td>

<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

</td>

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

<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">+</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

</td>

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

<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">--!!F!8!FF-!-!88!88!-!#8-FF#F888F!!F!8--8F-!FF8-!F-8FF!FF8F8!88#8--!888!-F!FF8F8F-F-F#!F!88F-F#8!!F8#-!8!---88!--88F-F-88F#8888#-F!#FF!##!F8-!-8F8F-8F-</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

89

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1452:1000 2:Y:0:</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

90

</td>

<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">AAGATCAATTTATGCACGGCCACTAGTGTGGTGAACACCTGTNGTAGTACTTGGTTTACGTCTCCNCTATCGTGCCGTAGAGTTCCCTGTTGGTATGTTATAGGGAACGGAGCATCTCATGCGCCAAACGAGTTTGACGNTGGAGCCNGTC</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

91

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">+</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

92

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">-8-FFF888F--F8--!8-!--!8F-FF--88F8FF-8-!!F#!-8-!88FF!F--FF!!F8-88#!-F-8---!!F8888!FF!F8!!!8---F88F8888FF!-F--F8-8F-!8FF--FF-888F-F8F-F-8-F-#!FF-8!8#!8!</span>

</pre>

</td>

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

93

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

</td>

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

<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1470:1000 2:N:0:</span>

</pre>

</td>

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

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

94

</td>

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

82

</td>

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

<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">GGGAATTCCGGTTTTTGGCGAAGTCTCGATAACTTCCGCGCGGCACCTAACTTGCCAGCTGTGGTTCGCGTCGTGANTTAATGTTGGGNTCTCGCNCGACATAAAANTGTAAAGGGAGGCCTTGGAGGCCCNGGTGTATGCTNCCAGCTGG</span>

</pre>

</td>

</tr>

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

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

95

</td>

<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

</td>

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

<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">+</span>

</pre>

</td>

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

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,10 +98,6 @@ TTTCACCAGGCCTCCTCGTAAGTAGATCTTATTTGGATCCAGGTAGCATCGGGGGAGCCGACATTNGTCCNGTCTCAGCG</td>

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

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

110

</td>

<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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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="LC98" class="line" lang="plaintext">TTCCTCGNACGTCTTTGNAGANTTTCGCCCAAGGCTTGTCCNTGCAAGACGTCCTGTCGTATAAACNGCCACGGGCGGCTAGGACTTGGANACGGACCTNATAGTTCCTGTGCCACTTNTCGNGTTTTCGTCTTGTTGNTGCGANAGGGGN</span>

</pre>

</td>

</tr>

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

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

111

</td>

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

99

</td>

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

<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">+</span>

</pre>

</td>

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

112

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

100

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

<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">F-!--F-#-8-F!-F--#-!-#88888F-FFF-F!8F!--!#-!-88-F!!F8!88-8-!8--F88#-F--F8FF!-F!!8F8FF8FF-F#--F-F8-F#F-F!F!!FF8!!F!88!F#!-!#-!--F8--!-8!8-8#F88-F#-8-F-#</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

113

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1054:1000 2:Y:0:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

114

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">GNGAGTAACNGGATTCGCCAGTAGTTGTTGCACTTGAANCTAACGCCATTTCGTCCACGGNTTTCTTCGAGNCGGAGGCCGTGGTCCCNNCGCGCAGATNGTTNNGAAGTACCGAGACTGGCCGTGACACTGCACNNCGGGANACCTCCGC</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

115

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">+</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

116

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">!#-8F88--#88-F8!--F8---!FF8!!FF8F8-FFF#88F8FF!!-!F!-FF!8F-8!#!8!!-!!--!#F8F-8FF!!F!-88--##!F!888F-!#-F!##!F-!--F!F8!F-F8F8FF!FFF888!88!##888-8#-!-!8F-F</span>

</pre>

</td>

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117

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

101

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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="LC101" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1072:1000 2:N:0:</span>

</pre>

</td>

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

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

118

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

102

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

<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">ANGAGGCNCCGCCCCNNTTNCTCGTNGCCCTCCCAACCGTGCGACTGGNNGCGCTGGACATCGTCGCAACTTACGGCGTGTGCCCTGAAGGTGACTACACCGNTGAAAGGNCGCCTCGCCGTCCATGCCACAAGGTGGACGNTCATCGNCT</span>

</pre>

</td>

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

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

119

</td>

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

103

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

<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">+</span>

</pre>

</td>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,10 +114,6 @@ TTTTCCAGTCNTTCTTGCAGGCCGGTGCATCGGCTTNACGCAATGNCCCCTCNACGTTGTGAGTGTCCCGATCAATTTGN</td>

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

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

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

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

<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext">CGCCGCTATTCCGGACANATNGTGTGACGCTTTCCGTCTCCCGTCGTCTCGATTTGGCGCCNATCNTCCGTCAGCCTAGAGNANTAACGAANCTGGATGCTGCNCATTGGANATGACTACCTGCTACTTGGNACGATTCTGCACGTCGTCT</span>

</pre>

</td>

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

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

131

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<td class="diff-line-num 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">

115

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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="LC115" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">!88F8FFF!8888!-8-#F8#-8!!F-!FFF!888--8FF-F-F--8-!FF8-F888-F!8#F--#!88!!-F-FF!F-8-#-#!--FFF-#8-8-8-!-!-!#88F!!8F#F!8FFF8-F---FF!-888#F8FF8------88--8F!-</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1145:1000 2:Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

134

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">ATAGATCCTGTTTAGCCGTTGTTGTTAGCCCCNTCTAGCNNATACCGAATCNGCCCTNCGATCTCCTCAGAGTTCGACCTTCCTTTCNGGAGAGGGTACCTCTCAGAANGCAAGGATGCCCATGTCACTCAGATCCTANATNAGAATCTTT</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">8-F8F-!-!F8F-F!!8--!8F8-F-8!-8!!#88-8F!##F-FF!!FF-8#F--8F#-!FF!F-FF8-F8!-!--F8!8!!88F8-#!!F!-F-88F888--8F!FF#---FF8F8-8!!-F!F!8!-F8-8!-F8-#F!#-FFF!-F-F</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1163:1000 2:N:0:</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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

118

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext">CCTGCTCCTCGGCCGACCTGNCCCTAATGCAGTTGCTCCGGANCTGCCAACGAAAACCTTACTCNTCTANCTCGTANACTACGGCACTGAAGCANTCNGCCCNTTTGTTCNCGTCTAACCACTCTTTCTTCGCGCGATNTAAGGCCTNCTC</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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

119

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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="LC119" class="line" lang="plaintext">+</span>

</pre>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,10 +174,6 @@ TCGGCACGACTACTAGTAGCACNCCGCCTGGGTCACNTAGCCTCAGTTGGCTCAAATTTGGCTGGAATGACTAATCATAT</td>

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

<td class="diff-line-num old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

194

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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

174

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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="LC174" class="line" lang="plaintext">CCCTATTGCACTTAGNGCGTGGAATCGCGGGATTNCGGCCCCCGNCAGTCGGCTATGATTCGANTCCATGCGTGCGTGTGTGCGTATCCCCACGTATAAGAGCGCGGACACTCCANCTGGGAACCAATCNCANTGACNTAGCCGACAATAT</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

175

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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="LC175" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="LC176" class="line" lang="plaintext">-8F-F8!F-F8-888#F8FF!!F8F!-8!8!8F-#8F!--8F!F#-8!F!8!-F8-!8F-FF-#-8--8!!88-----F-8--!!888!-F8!-88-----!8!88!8-8-!!-F#!--8!8-!!8--F#!-#F!--#F-F!-!-!F-F88</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1452:1000 2:Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext">GCGNCGCTTCGNGNCCGGATGACCTGCTTTGTTNCTCAGTTTTTTTTATGNTNGTACATTCTTCCCTCGATCGAGTGTGTTTGCCTGCGGCTTAGTCGTGGGCTCGCGNCTGTNCGAGGCTGTCATTCCAGGCCTGCCAANNCGGCGGTCT</span>

</pre>

</td>

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199

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext">+</span>

</pre>

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200

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext">!-F#-8!-F!!#-#-!!F-88--!F8F88F--!#FF-8!8!-F8F--8F-#!#8888FF!F!!-F!F!--!!--!88F!8!8!F-!FF!F8!-FF-88-F-!F8-!F-#-8F!#FF888!!!-88-F!!F!-FF8!!F--##8F!---F!F</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1470:1000 2:N:0:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

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<td class="diff-line-num new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext">AAGCAANGANGACACCGGTGTCAGTGTTTTGGNATCGCAGCTTTNGACCTGCTTCCTNAACTTNTCTGTTTCCGAAGTCACTTATTNTAAACGAGCTCTGGACTAGGCTCTGTACTCCCAATCTCGTNNTCTCGGGTCAANGAGCCTGGCC</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext">+</span>

</pre>

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<br>

</li>

<li id="0b36bda2a264efe61db7b14ff0b709022f11e824">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#0b36bda2a264efe61db7b14ff0b709022f11e824"><strong>testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.barcode_1.fastq</strong></a>

<hr>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,10 +6,6 @@ FF!#F-!F</td>

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

6

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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

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

</pre>

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

7

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7

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">+</span>

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<td class="diff-line-num 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">

8

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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">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">FF-!F888</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1054:1000 :Y:0:</span>

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10

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</pre>

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

11

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">+</span>

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12

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">!!FF8F8-</span>

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

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

9

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1072:1000 :N:0:</span>

</pre>

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

14

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

10

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

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

</pre>

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

15

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

11

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">+</span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -26,10 +22,6 @@ AGCCCCCT</td>

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22

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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="LC22" class="line" lang="plaintext">CACTTTTC</span>

</pre>

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

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

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

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">FF88F!8F</span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1145:1000 :Y:0:</span>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

</td>

<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">GTAGGGAT</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">+</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

32

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">F--!!8-F</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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

25

</td>

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

<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1163:1000 :N:0:</span>

</pre>

</td>

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

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

34

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

26

</td>

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

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

</pre>

</td>

</tr>

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

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

35

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

27

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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="LC27" class="line" lang="plaintext">+</span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -86,10 +78,6 @@ TAGCGTTN</td>

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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

86

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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

78

</td>

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

<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">AATTTGCG</span>

</pre>

</td>

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

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

87

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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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="LC79" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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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="LC80" class="line" lang="plaintext">-F--8!!!</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

89

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1452:1000 :Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

90

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">TCGGCAAC</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

91

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

92

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">8F8-8FF-</span>

</pre>

</td>

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

93

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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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="LC81" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1470:1000 :N:0:</span>

</pre>

</td>

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

94

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

82

</td>

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

<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">GANCGAAC</span>

</pre>

</td>

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

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

95

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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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="LC83" class="line" lang="plaintext">+</span>

</pre>

</td>

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

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,10 +98,6 @@ TCGTNTTG</td>

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

110

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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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="LC98" class="line" lang="plaintext">NCATATCT</span>

</pre>

</td>

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

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

111

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

99

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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="LC99" class="line" lang="plaintext">+</span>

</pre>

</td>

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

112

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

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

<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">#!FF-!!-</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1054:1000 :Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

114

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">CTTATTTA</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

115

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">+</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

116

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">8!!---FF</span>

</pre>

</td>

</tr>

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

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

117

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

101

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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="LC101" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1072:1000 :N:0:</span>

</pre>

</td>

</tr>

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

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

118

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

102

</td>

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

<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">CCCATGCC</span>

</pre>

</td>

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

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

119

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

103

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

<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">+</span>

</pre>

</td>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,10 +114,6 @@ CCCGNGCT</td>

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

130

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

114

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

<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext">GTGGCAGA</span>

</pre>

</td>

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

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

131

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<td class="diff-line-num 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">

115

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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="LC115" class="line" lang="plaintext">+</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

132

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

116

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

<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">8F8-FF88</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

133

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1145:1000 :Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

134

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">GGTAAGGT</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

135

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">+</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

136

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">F!8---8!</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

137

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

117

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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="LC117" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1163:1000 :N:0:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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

118

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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="LC118" class="line" lang="plaintext">CCGCGCNC</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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

119

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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="LC119" class="line" lang="plaintext">+</span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,10 +174,6 @@ TTAGCGTG</td>

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<td class="diff-line-num old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

194

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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

174

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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="LC174" class="line" lang="plaintext">TNNGAGAA</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

175

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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="LC175" class="line" lang="plaintext">+</span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

196

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<td class="diff-line-num new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

176

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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="LC176" class="line" lang="plaintext">F##-F!88</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

197

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1452:1000 :Y:0:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

198

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext">GGGGCACT</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

199

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext">+</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

200

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext">-8!-!FF-</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

</td>

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

<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1470:1000 :N:0:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

</td>

<td class="diff-line-num new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

</td>

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

<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext">GGGCAAAT</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

</td>

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

<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext">+</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8506191367e07f8a80c6a0d9b26eb280edb3ac94">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#8506191367e07f8a80c6a0d9b26eb280edb3ac94"><strong>testdata/picard/illumina/151T8B8B151T_cbcl/fastq/NN.barcode_2.fastq</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,10 +6,6 @@ CCTGGTAC</td>

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

6

</td>

<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

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

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

</pre>

</td>

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

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

7

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

7

</td>

<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="plaintext">+</span>

</pre>

</td>

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<td class="diff-line-num 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">

8

</td>

<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">

8

</td>

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

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">F8-F!-#-</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1054:1000 :Y:0:</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

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

</pre>

</td>

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

11

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">+</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">FF--88F-</span>

</pre>

</td>

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

13

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

9

</td>

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1072:1000 :N:0:</span>

</pre>

</td>

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

14

</td>

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

10

</td>

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

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

</pre>

</td>

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

15

</td>

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

11

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">+</span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -26,10 +22,6 @@ F8F#-!--</td>

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

26

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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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="LC22" class="line" lang="plaintext">GTTGTAGG</span>

</pre>

</td>

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

27

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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

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

</pre>

</td>

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

28

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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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="LC24" class="line" lang="plaintext">-!!F-88!</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1145:1000 :Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">AGCCGGCG</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

32

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<td class="diff-line-num new_line old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">FF!F88-F</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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

25

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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="LC25" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1163:1000 :N:0:</span>

</pre>

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

34

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

26

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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="LC26" class="line" lang="plaintext">CTGCGTAC</span>

</pre>

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

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

27

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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="LC27" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -86,10 +78,6 @@ ANCGGGCT</td>

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<td class="diff-line-num old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

86

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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

78

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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="LC78" class="line" lang="plaintext">AGCAGNGT</span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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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="LC79" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(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="LC80" class="line" lang="plaintext">8!!88#!-</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1452:1000 :Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">CCNATNCT</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">8-#8-#88</span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(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="LC81" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1101:1470:1000 :N:0:</span>

</pre>

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

94

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

82

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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="LC82" class="line" lang="plaintext">AGNTGGCN</span>

</pre>

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

95

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">+</span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,10 +98,6 @@ CGTGGATT</td>

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

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">ANAGGCCG</span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">+</span>

</pre>

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

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

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

<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">8#88!!F!</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1054:1000 :Y:0:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

114

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">GGCTNTAG</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

115

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

116

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<td class="diff-line-num new_line old" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">-!88#888</span>

</pre>

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

117

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

101

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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="LC101" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1072:1000 :N:0:</span>

</pre>

</td>

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

118

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

102

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

<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">GATGTTTA</span>

</pre>

</td>

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

119

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

103

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

<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">+</span>

</pre>

</td>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,10 +114,6 @@ CATCCNTG</td>

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

130

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

114

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

<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext">GAAACGAA</span>

</pre>

</td>

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

131

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<td class="diff-line-num 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">

115

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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="LC115" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

132

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

116

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

<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">F-8-8-FF</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

133

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1145:1000 :Y:0:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

134

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">TCCACGTT</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

135

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

136

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">!8-F!F8!</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

137

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

117

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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="LC117" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1163:1000 :N:0:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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

118

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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="LC118" class="line" lang="plaintext">NGGGATAT</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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

119

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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="LC119" class="line" lang="plaintext">+</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,10 +174,6 @@ F-F-88F!</td>

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<td class="diff-line-num old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

194

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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

174

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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="LC174" class="line" lang="plaintext">TTACGCGC</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(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="LC175" class="line" lang="plaintext">+</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="LC176" class="line" lang="plaintext">!!FF!8!8</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

197

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1452:1000 :Y:0:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

198

</td>

<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext">GGCCCGCT</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

199

</td>

<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext">+</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

200

</td>

<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext">!F-F--F!</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

</td>

<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

</td>

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

<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext">@machine1:HiMom:abcdeACXX:1:1102:1470:1000 :N:0:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

</td>

<td class="diff-line-num new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

</td>

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

<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext">CTGGTNNN</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

</td>

<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

</td>

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

<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext">+</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="3aadcdc6893bc7af006edf8906d071b5dc87b7d3">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#3aadcdc6893bc7af006edf8906d071b5dc87b7d3"><strong>testdata/picard/illumina/151T8B8B151T_cbcl/sams/1102.NN.sam</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,8 +6,6 @@ HiMom:1:1102:1018:1000 77      *       0       0       *       *       0       0       .GGAAA.GGATAA.CCAGACACCCAA.GGATATGTAGCAT</td>

</tr>

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

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

6

</td>

<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">HiMom:1:1102:1018:1000        141     *       0       0       *       *       0       0       TTTCACCAGGCCTCCTCGTAAGTAGATCTTATTTGGATCCAGGTAGCATCGGGGGAGCCGACATT.GTCC.GTCTCAGCGTCGTCCACCTACTCTGACG.GTACCAGAGTGCTCCCGGTACCTCAGTGCCAAGTCGGATTAGCTTGCCAGT 88!!8-8F-F-F-8-!!-!F88F-F-8!FF-8F!8!F!8FF-FF88-F8!F!!8-F!F8FF8FFF#!8!F#8888!-8-!!F-F!F-F8!-!88!--F-#!F88!F!-!F!8-8F!!-!F!--F--F8-!8888F!!8F88!!----!888 BC:Z:TCGTNTTG-CGTGGATT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

7

</td>

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

7

</td>

<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="plaintext">HiMom:1:1102:1036:1000        77      *       0       0       *       *       0       0       CAGTGTTTGTTCGAATCCGCTCCCTTCTGCTGACGTGGGT....GG.AACCGAAACGCTTTTCTCCCAC.CCGG.GTCGTTCAACTCTA.ATGGGACAGCGCATGGTTCGTCTA.GC.TGACTCGTGGCA.ACGTCCTACGACCGCTAAAT F-!8--!F-F-8!F8F888!!!F8!F-8F!!F-F-F!-!F####!!#-FF8!F-F!8FF--8F-8FF-!#!--F#FF-!8FFF---F!-#8-F!!8!--F!FF8-88FF8--88#F-#!!-FF!F---!F#8F--88!F-!--!8!8F8-8 BC:Z:NCATATCT-ANAGGCCG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num 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">

8

</td>

<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">

8

</td>

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

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">HiMom:1:1102:1036:1000        141     *       0       0       *       *       0       0       TTCCTCG.ACGTCTTTG.AGA.TTTCGCCCAAGGCTTGTCC.TGCAAGACGTCCTGTCGTATAAAC.GCCACGGGCGGCTAGGACTTGGA.ACGGACCT.ATAGTTCCTGTGCCACTT.TCG.GTTTTCGTCTTGTTG.TGCGA.AGGGG. F-!--F-#-8-F!-F--#-!-#88888F-FFF-F!8F!--!#-!-88-F!!F8!88-8-!8--F88#-F--F8FF!-F!!8F8FF8FF-F#--F-F8-F#F-F!F!!FF8!!F!88!F#!-!#-!--F8--!-8!8-8#F88-F#-8-F-# BC:Z:NCATATCT-ANAGGCCG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">HiMom:1:1102:1054:1000        589     *       0       0       *       *       0       0       CGGG.CCGCCAGAT.TTCCCCGTTCCCACGGACGTTCCTTGGCAGCGCTACTGTCGGGGTTGATCATGCCGGTGTAGCAGGCGT.CCGGACAGTGAACTAA.GTCTTGATTCCACCG..CATAGC.TCTGATACACCTCAATTCGAGTTCA --8-#-8F8FF-FF#--F8!--8--F8F!!F88F-!!F8!!8--F8F888F8F!--8!88F-F88--!F88-F!--FF-8-FF!#F!-88F-8FFFF-!-F#-F8!-!8!!-88!F-##!F-88!#F-F---FF8FF8!8F-8F-F!-8!8 BC:Z:CTTATTTA-GGCTNTAG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">HiMom:1:1102:1054:1000       653     *       0       0       *       *       0       0       G.GAGTAAC.GGATTCGCCAGTAGTTGTTGCACTTGAA.CTAACGCCATTTCGTCCACGG.TTTCTTCGAG.CGGAGGCCGTGGTCCC..CGCGCAGAT.GTT..GAAGTACCGAGACTGGCCGTGACACTGCAC..CGGGA.ACCTCCGC !#-8F88--#88-F8!--F8---!FF8!!FF8F8-FFF#88F8FF!!-!F!-FF!8F-8!#!8!!-!!--!#F8F-8FF!!F!-88--##!F!888F-!#-F!##!F-!--F!F8!F-F8F8FF!FFF888!88!##888-8#-!-!8F-F BC:Z:CTTATTTA-GGCTNTAG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

11

</td>

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

9

</td>

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">HiMom:1:1102:1072:1000        77      *       0       0       *       *       0       0       GCGCTTGTTCCGATTTGT.TGGCGCTGCGGCAGCCTGATCGG.GCGCCTTGGT.GAGAGGCGCACTTGCACTA.CG.CGGGCTACCGCCA.ACGTTTTCTCTGCCGG.AGCCGTATCCGGTTGGAT.TTCCG.CCATCCACGAACTTCATC F---F!!-!8!F8F8--F#8F-8888!!--F8!-88-F88FF#!88F-F-FF-#FF-F-FF!-F-!FF!8--F#-!#F8FF-F8!FFF!-#F!F8F8!8FFF8!-88#--8!FF8F-8!F8-!8-F#8-!--#FF8!!--!!FF8FFF8!- BC:Z:CCCATGCC-GATGTTTA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

12

</td>

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

10

</td>

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">HiMom:1:1102:1072:1000       141     *       0       0       *       *       0       0       A.GAGGC.CCGCCCC..TT.CTCGT.GCCCTCCCAACCGTGCGACTGG..GCGCTGGACATCGTCGCAACTTACGGCGTGTGCCCTGAAGGTGACTACACCG.TGAAAGG.CGCCTCGCCGTCCATGCCACAAGGTGGACG.TCATCG.CT 8#--8F-#F8!F!F8##88#-!F-8#F!-F---FF-F8-!8-8-8F8!##--F-F-8FF-FFFF--8--!8--F--!FF!!-!888FFFF!!!-!--F-8!-#--8FF!-#FF-!8F!-F-!-!8-888FFFF-8!--8!!#-F-8F!#!8 BC:Z:CCCATGCC-GATGTTTA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

13

</td>

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

11

</td>

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">HiMom:1:1102:1090:1000       77      *       0       0       *       *       0       0       GCCTACGCATCCGCCC.CACTG.ATGGGTGAGCC.G.ACTAAGCTGTAGTGCCTGATCCCTCCAGGAGCCCTTTA.TGAATCGGAACGCTATGCGACTTGTGATAACGAAAATTTCAGAAGTT.ATCGCCAGTGTGGTTCTTCC.AACATG !-F-88F88!!8!--8#---8!#F8F8-!F--8!#8#8-8F-8-!-F888FF8!8F88!-F-F8!8F---!F8!-#8F-F8!F--8F!!!8-F8F8FFF!!!---8!-8FF8F!-8-!FF!F-#-FFF88-8!!8!!8-8!F-!#FF!8!- BC:Z:TTGCCTTT-TTTCGGTA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,8 +14,6 @@ HiMom:1:1102:1108:1000       77      *       0       0       *       *       0       0       TTA.GGGGAGTGC.AAGG.CTTA.AGTTCACCGAGCCCAT</td>

</tr>

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

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

16

</td>

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

14

</td>

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">HiMom:1:1102:1108:1000       141     *       0       0       *       *       0       0       TTTTCCAGTC.TTCTTGCAGGCCGGTGCATCGGCTT.ACGCAATG.CCCCTC.ACGTTGTGAGTGTCCCGATCAATTTG.GC..AAGTACCAAAGGTGCCTGTCTGTAGTTGAACATTACGTGGCGTATGG.GTAAGTTTCTATGCACGCG 8FF-8F8-88#F8--8F!F--8888F-8F!!--!8-#8-8-8--8#8-8F!F#8!F-F-8!--!8-!!8!88!-F!!8-#--##F--8-!-8-F!FFFF88!8-8FFF-!F8FF8FF-F!--F88-!-!!8#-F88!F8F!8-F-8-F--- BC:Z:CCCGNGCT-CATCCNTG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

17

</td>

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

15

</td>

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">HiMom:1:1102:1127:1000       77      *       0       0       *       *       0       0       GCC.AACGATCTT.TTTGCTC..CGTG.TGCTTGGTCTTCTTGTCTCTAACTA.CGTGTAGTGAGAGT.TCTCTCTCGAGCGT.TCTGGATTGC.CGACGGACGAGGAATTAGTGCTCAGTGTATCGGACC.TTTTCTGGCCGCATGCAGC 8!-#8-8!-F!-8#!8-!88-##8-FF#FFFFFF!!F-F-F-FF!F--8-8-8#!!!!!88-!F-F-!#8---88!FF8-FF-#-!8-!88-8!#!8--F-FF8FF88F!F8F8!!8!-F!88-!!-F8!F#!8---!-!F!--8--!F!8 BC:Z:GTGGCAGA-GAAACGAA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

18

</td>

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

16

</td>

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">HiMom:1:1102:1127:1000       141     *       0       0       *       *       0       0       CGCCGCTATTCCGGACA.AT.GTGTGACGCTTTCCGTCTCCCGTCGTCTCGATTTGGCGCC.ATC.TCCGTCAGCCTAGAG.A.TAACGAA.CTGGATGCTGC.CATTGGA.ATGACTACCTGCTACTTGG.ACGATTCTGCACGTCGTCT !88F8FFF!8888!-8-#F8#-8!!F-!FFF!888--8FF-F-F--8-!FF8-F888-F!8#F--#!88!!-F-FF!F-8-#-#!--FFF-#8-8-8-!-!-!#88F!!8F#F!8FFF8-F---FF!-888#F8FF8------88--8F!- BC:Z:GTGGCAGA-GAAACGAA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">HiMom:1:1102:1145:1000       589     *       0       0       *       *       0       0       AGATTTGTCAGAGTGT.T.TCAGCGGTA.CGTAGTAGGCGGTGTTGGGCCGGTTC.T.TA.TG.TCGAGCAAG..ACGGGCACACTG.CCATT.ATCCT.ATGCAAAAGC.TGG.CCC.TGGGAGGAGCCTAGCGAGCGGGGGCGTTTTTA 8-F-8FF88F!-!F!F#!#!-F-8F!!-#8F888-F!8!8!!8!888-!F!FF!-#F#8-#!F#F-!88-8F!##-F--!--FF-8F#!8FF8#--FF-#8F!-FFFF!8#8!F#-!-#8-FFF!8-FF!8-8--FF!-!8-!!F!!-8-- BC:Z:GGTAAGGT-TCCACGTT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">HiMom:1:1102:1145:1000       653     *       0       0       *       *       0       0       ATAGATCCTGTTTAGCCGTTGTTGTTAGCCCC.TCTAGC..ATACCGAATC.GCCCT.CGATCTCCTCAGAGTTCGACCTTCCTTTC.GGAGAGGGTACCTCTCAGAA.GCAAGGATGCCCATGTCACTCAGATCCTA.AT.AGAATCTTT 8-F8F-!-!F8F-F!!8--!8F8-F-8!-8!!#88-8F!##F-FF!!FF-8#F--8F#-!FF!F-FF8-F8!-!--F8!8!!88F8-#!!F!-F-88F888--8F!FF#---FF8F8-8!!-F!F!8!-F8-8!-F8-#F!#-FFF!-F-F BC:Z:GGTAAGGT-TCCACGTT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

21

</td>

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

17

</td>

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

<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">HiMom:1:1102:1163:1000       77      *       0       0       *       *       0       0       GATACGGTGTTATTCTTCTTGATTTGACTACG.GTCCGACAAC.TATTCGTGGAAACACGGCCCAATAGCGCT.GCCC.ACAGCTTTATAGTGTCA.CAGTGATTACGTCG.TGTCAGGGTTTACAATG.AG.GCAAGCGTTTGGCGGCGA !-!888F-8!!8!8--88!888---!8FF88F#--!F8-!-F8#F88F!88!!F-8F8-8!--!-F!FF!8-F#F!!8#-!F88F-!-FF!8FFFF#F-88F8F!8!!8FF#!8-!F888F8F--FF8-#88#-!--F88F!-F-!--!F- BC:Z:CCGCGCNC-NGGGATAT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

</td>

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

18

</td>

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

<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">HiMom:1:1102:1163:1000       141     *       0       0       *       *       0       0       CCTGCTCCTCGGCCGACCTG.CCCTAATGCAGTTGCTCCGGA.CTGCCAACGAAAACCTTACTC.TCTA.CTCGTA.ACTACGGCACTGAAGCA.TC.GCCC.TTTGTTC.CGTCTAACCACTCTTTCTTCGCGCGAT.TAAGGCCT.CTC F!-!-F88FF-!F-88F!-!#-8!8-F!88--8F!!FF--8F#-FF88FF---F8F8!88F8!-#F!!8#88!-FF#-!FF8!F-F!88F----#!-#-!F-#8!--!!8#88FFF88F8-8!!-!F888!!FF!8F8#8-F!!!-8#F!- BC:Z:CCGCGCNC-NGGGATAT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

</td>

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

19

</td>

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

<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">HiMom:1:1102:1181:1000       77      *       0       0       *       *       0       0       TAGCATCGTAAACGGGACTTCGCTAGTCCAGTCTCTTACTAGTCCGG.T.TGGACTA..GTT.TGTA.ACCCGACTCGGA.T.CATTAGTCAC.CAGACT.CTGT.G.CATCAA.GACCC.AC.CCTCCTTCCCAGATAACCGTT.GTTTC -F!!8F!F!F--!F-F--F!-!---8F!!F-FF-!F8F8F--F--8-#-#-8!F!!F##-88#-8F8#-!-8F--!-!!8#8#8-!F88-8--#-F--!-#!---#-#F-8FFF#8888F#8!#F-888!!!-FF-F!FFF!!!F#8!F88 BC:Z:CGCGTAGT-ATTCCGAC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,8 +44,6 @@ HiMom:1:1102:1416:1000       77      *       0       0       *       *       0       0       TGACTACTTAGTAACGG.G.CCGTGGCCGCTACTGCGCCG</td>

</tr>

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

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

48

</td>

<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

</td>

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

<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">HiMom:1:1102:1416:1000       141     *       0       0       *       *       0       0       TCGGCACGACTACTAGTAGCAC.CCGCCTGGGTCAC.TAGCCTCAGTTGGCTCAAATTTGGCTGGAATGACTAATCATATTTTGTCCATACAATCGATCTTTGGGCCTCCC.CCCCAT.A.CCGCGGGGTACCTTGTGCCTCTCACTTGCC -8!FF8!!8F8F8F-!!F8-8F#FF88!8-!!!FF-#-F8FF8F-FF-F-8-!8FF88!8-88-88F!-F!F888888-!!F8F!!FFFFF---!FF!-!F88--8---!F#-!8FF!#F#!-8!--!FF-!!F88!8FF--!88F88F!! BC:Z:TTAGCGTG-GTGCCAAG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

49

</td>

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

45

</td>

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

<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">HiMom:1:1102:1434:1000       77      *       0       0       *       *       0       0       CGGGGACAGTGTCATTATCGCC.CCG.GCAGG.TTAAG.C.T.CCGG.GGGGGCAGTGCTATTCCGATGTCCCCG.AATAGTC.TGGGTCAGTACCCATGCCCCTTATA.AGC.ATAT.GTAG.CAGCGGCTTGCGGCTCAGCCCATTTTA -8-8---F!8!-8-!!FF8!!-#8!-#8F-F8#F--8F#-#8#FF8F#-8FFF8-!8-!-8FF!-!-88F88!-!#8F8F-FF#!!-F888-F-!-888!FF!8FF8F-#88!#888!#8FF8#!888!-88!!8--8!!-8-FF-88!8F BC:Z:TNNGAGAA-TTACGCGC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num 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">

50

</td>

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

46

</td>

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

<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">HiMom:1:1102:1434:1000       141     *       0       0       *       *       0       0       CCCTATTGCACTTAG.GCGTGGAATCGCGGGATT.CGGCCCCCG.CAGTCGGCTATGATTCGA.TCCATGCGTGCGTGTGTGCGTATCCCCACGTATAAGAGCGCGGACACTCCA.CTGGGAACCAATC.CA.TGAC.TAGCCGACAATAT -8F-F8!F-F8-888#F8FF!!F8F!-8!8!8F-#8F!--8F!F#-8!F!8!-F8-!8F-FF-#-8--8!!88-----F-8--!!888!-F8!-88-----!8!88!8-8-!!-F#!--8!8-!!8--F#!-#F!--#F-F!-!-!F-F88 BC:Z:TNNGAGAA-TTACGCGC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

51

</td>

<td class="diff-line-num new_line old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">HiMom:1:1102:1452:1000       589     *       0       0       *       *       0       0       GTTCCGGACGAAGGACTGGATTGCTGCTCAGAGATCCCGGTTCCAGGGTCGGT.CAATTTGTCCGCCAGGTGGA.CTTGTTCTTTCAGACTAAGGTT..AGTGA.GCCAGCATTAAGATACAGAAACAACTCGTCCCCT.TCTGACGATCA 8-FF8!---FF8!!8!-F!8F!8--FF-8F!F!F!!!F-!8F!-8F8F!8!88#FF-88FF!-!-8!F8-!!--#!!-FFF-F8F8--8-F--8!-!##-F!8F#-88F8F-!F-F8F!8-8-FFF8FF-8F-!88!8!#-8F8-8F---F BC:Z:GGGGCACT-GGCCCGCT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

52

</td>

<td class="diff-line-num new_line old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">HiMom:1:1102:1452:1000       653     *       0       0       *       *       0       0       GCG.CGCTTCG.G.CCGGATGACCTGCTTTGTT.CTCAGTTTTTTTTATG.T.GTACATTCTTCCCTCGATCGAGTGTGTTTGCCTGCGGCTTAGTCGTGGGCTCGCG.CTGT.CGAGGCTGTCATTCCAGGCCTGCCAA..CGGCGGTCT !-F#-8!-F!!#-#-!!F-88--!F8F88F--!#FF-8!8!-F8F--8F-#!#8888FF!F!!-F!F!--!!--!88F!8!8!F-!FF!F8!-FF-88-F-!F8-!F-#-8F!#FF888!!!-88-F!!F!-FF8!!F--##8F!---F!F BC:Z:GGGGCACT-GGCCCGCT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

53

</td>

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

47

</td>

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

<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">HiMom:1:1102:1470:1000       77      *       0       0       *       *       0       0       CAGACCGCGGCTCTGGATCACCTCCGACGGGTAGTGACA.CTACCT.AATCCGTCCAAGCAATGTGCAGTTCTTAATGACTTGGCTCGAGTAGTCCTGACCAA.GAACGGACGTTCTTCGA.GATAGGTGGGAG.TGGCTTCACGCTTTAC 8FF8-FFF!F-8--F-888-!!-!-8--8FFFF!!F8FF#!!F!!8#F8!8F8-8-8-F!--8-F!8----!F----8-8-F!!-F!F-!F-!!F-F!FFFFF#F--F----!!F-!!F--#88!F!F!8-F--#-F8-F-!-!!-!!!-F BC:Z:GGGCAAAT-CTGGTNNN  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

</td>

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

48

</td>

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

<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">HiMom:1:1102:1470:1000       141     *       0       0       *       *       0       0       AAGCAA.GA.GACACCGGTGTCAGTGTTTTGG.ATCGCAGCTTT.GACCTGCTTCCT.AACTT.TCTGTTTCCGAAGTCACTTATT.TAAACGAGCTCTGGACTAGGCTCTGTACTCCCAATCTCGT..TCTCGGGTCAA.GAGCCTGGCC F8-888#!8#-8--F--!F--888!8F8!-F8#-F!!!--!F8-#--8--F-!8FFF#--F!-#!F-!!!F-8-FF8--F!-88!8#88-F-F-8F--!8!F!-8-F--!88FF!-8!--8-!88F!##-!8-!!FF8-F#8FF-!!!--- BC:Z:GGGCAAAT-CTGGTNNN  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

55

</td>

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

49

</td>

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

<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">HiMom:1:1102:1488:1000       77      *       0       0       *       *       0       0       CGCTGTGCGTAACTTCCATGAATATCGAGGTGGATCTC.GTAGTGTTTG.AC.ATAGGTACAAACGTCCAACATGTCACGTCGAGAACGCCCCGATGTGCGCGAGAAGT.ATGAGCGTATGCAGGGCGTCAATTGCCCTTGAGAAGGTGGG FF--8F88!!-8-F8!-FF!88F-!F8F!F!!F--F88#!88-F-F--F#8-#8-8-8-8!F-88!8!!FF88!FF!-8FFF--8-8F8-FF8--8FFFFF-FFF8888#F8!F!888-F!--!88-8!---FFF-!!F!FF--8F88-!! BC:Z:CTCATACG-CTGNTCCC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="e5f7bc4229f0f1ed297e3bf5c17fa7773b2e182d">

<a href="https://salsa.debian.org/med-team/picard-tools/commit/2d8023c38e442005719ef005b4a3d47b51154968#e5f7bc4229f0f1ed297e3bf5c17fa7773b2e182d"><strong>testdata/picard/illumina/151T8B8B151T_cbcl/sams/NN.sam</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,8 +4,6 @@ HiMom:1:1101:1000:1000 77      *       0       0       *       *       0       0       TGATGGTTTCGGG.TTTAGACAGTGTCATGCCTATTCC.T</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">HiMom:1:1101:1000:1000        141     *       0       0       *       *       0       0       CCTGAAGAG.C.CA.C.CCA..GGATGA.AGTGACCACGGGATGC.AGTGCCCACGATGCGTAGGACGGGGAGCCATGATCGTCCGGGTTTGGCGT.CTATCGTGATAGGAGACGGTGCCCAGTGATGCC.CCGCGCACTG.TAACCCAGT F-!F8--8F#F#88#-#-FF##F-8!-8#88-F-F-F8F-F-F8F#-8!--8F8-!F!8F!--8-8!FFFFF8F!FFF-F-8-FFFF!8--88!8-#88F!88-F-F-F-FFF8--8--!!-FFF-F!!!#FF8-FFF!--#FF-F!-F-! BC:Z:GCCNAGTA-CCTGGTAC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

5

</td>

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

5

</td>

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">HiMom:1:1101:1018:1000        77      *       0       0       *       *       0       0       GGTGGGGCAGCTC..GT.CTGGGTATG.TTACATGATTCAAGCATACTGCCCCTGATA.TA.TCGCGG.TTCTGCTA.GTATTTCCCGGGAACTTCTTTCACCTATCCGAACAACAGCTTTCCCAGTCAGAGTCAGCGAACATTATAACTC FFF!-!-!F!!!!##!F#!FF8!FF-!#8!8F-8!----F-!-F8--88-FF!-!8F-#88#-8F!8F#88-8!!FF#!F8!8!!F!F-F-F!8F8FF!8---8-FFF8---8-8--!!-F8-!8888F8F8!F8FFF--!F!-8FFF--F BC:Z:CTTCGTGT-TATGCANC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

6

</td>

<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">HiMom:1:1101:1018:1000        141     *       0       0       *       *       0       0       CCTCG.TAGGATCATCCTCGCGTGCCATCGC.GATACT.GCTTTATAACTTTTTAATACCACCACTTAAAGC.TTAG.T.TGCACAAGGTCGTACTAAAGGACCCGCTAGCGCGTGATCTGTGGTCCCACAGAGTAC.CCGACTACT.TTA FF!8F#F88F-!F88--FF----8-F88FF8#!88-!F#-FF-8FF--88!F!FF8FF!8-F--8-!88888#!-8!#F#88F888-!--F--888F-8F-FF8F8---88!F!-FF!-!--FF--F88!-!-!FF!#!88F-88F-#88F BC:Z:CTTCGTGT-TATGCANC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

</td>

<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">HiMom:1:1101:1054:1000        589     *       0       0       *       *       0       0       GTCGTACG.TCGAAG.TGAGGACGGGATTGTCTGTAAACTTGCGCGAGACCGAAATGTCAAACGG.TTCGGTAACAAGAACACAAC.CTTCCGCATACACGTCGGTGTTTCCTATACCGCAACCGTTGGAGGTTCCACGG.CTAGGCTCGC F!!!8--8#88-FF!#--FF-88-88F-!8!F-!--F8F8!FFF8-8!F8F8FF--F-!F--F-F#-8!-F-FF8888F-----F8#!F!!8F!-8F!FFF!-!!---F--88-88-F8F-F!----FFF!!8F!8FFF-#8-88-!F-88 BC:Z:GGTGCGCG-GTGCAGAC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">HiMom:1:1101:1054:1000        653     *       0       0       *       *       0       0       AA.ACT.CGATTTTGAGATCATGCTCTACTT.CTGGCTATGTATGGTAGTGCGCTGA...TCTCTATTTTGTGAACATGGCT.GTCGT.GGGTGTCATCGGCTC.CCGTAACACT.TAGCCC.TGGGCCCGCGG.TG.AATTGCTGGGAGG -F#8!8#-F8---!F8888-8F-F---F888#!FF!F!--!!8FF8F8!F8FF!8--###F!F-!8!-F8F!-F--F!8!8F#88!--#!--8!-8--8-F8-8#!8---F8-88#!-FFFF#--F--!-!-!F#8!#F8F---8FFFFFF BC:Z:GGTGCGCG-GTGCAGAC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

9

</td>

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

7

</td>

<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="plaintext">HiMom:1:1101:1072:1000        77      *       0       0       *       *       0       0       CCTTGATC.CTCCGCTTGAGTTT.GTTTCAGATGCCTT.AGGAAGCGATATTCCAACTCATGGAGCGTCAGCAGCGATTGTCGTATAGCCGGGCAAATCACTAGGAATGCC.T.TGTGAACAGTGGCATTGTTGTATGGTGTGTCCCCAAG -F-F88--#F8F888-!8F!F--#-!-F8--8!FF!-8#F8-F8-F88!-F8-8--!FF8FFF-F88!!F8!-!8--8-!!!-F--F!F----FFFF!-8!8-F-F-8F8!#-#--8F--88-!-!!88-!F-!FFFF8F8F8F!-88FF8 BC:Z:CTTCCTTG-GTGTCTCG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

10

</td>

<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">

8

</td>

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

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">HiMom:1:1101:1072:1000        141     *       0       0       *       *       0       0       .CGG.CTGGTACCTATCGCGACGTCCACATTGTTGTATTC.GTT.CACAACCGTCTAGCCTTCT.TACTACCGCTAAGCTTAAA.CCAACTGGACAGTGGGACACGGCT.CTC.GTCACAAACACC.ACACAGCCTGTGC..CACCTCAAG #FF!#F-8--8!-8FF-!-F--8!FF88-!-8-!-8-!!8#F8!#F--8-!8!--F88-F!F!!#88!8-F!----8888!-8-#88F-FFFF8!FF!!8F-8F8FF--#-F!#!!-8-88888--#FF8-FF---!!8-##-88!-F8-- BC:Z:CTTCCTTG-GTGTCTCG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

11

</td>

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

9

</td>

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">HiMom:1:1101:1090:1000        77      *       0       0       *       *       0       0       G.ATAGG.AA.GGAGC.CCTGTAAAGTGCCGGTACATTGAATACCTCTCA.ATG.CAGAAGTAGACCAGCTTCG.CAGGACAAATTCATCATAGTTTATAGGTAATCCA.TTGAGGC.CCTTGGCTTGATATTCTCCCGTCTACCGAGTCT F#F-F-!#-8#!8---#F8!!F8-F8F-!8-!8-!8!F!F-88F88-F--#FF-#--88-!8F--FFF!8-8!-#FFF8F88F-!!--!!F!8!--88F-F8F8--!--#88!F8-!#F!8!F88F-F-F-FF8FFF8F-!!F8-!-!F-8 BC:Z:TCTCACTC-AAGAGCAA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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">@@ -14,8 +12,6 @@ HiMom:1:1101:1108:1000       77      *       0       0       *       *       0       0       .TCT.A.ATTAAGTGCGGCAG.TGGGGCCCCCTGGTTTGA</td>

</tr>

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

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

14

</td>

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

12

</td>

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

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">HiMom:1:1101:1108:1000       141     *       0       0       *       *       0       0       TGTGTG.ACTATCAATCGACCAGTACTTAGTTCAGCACCGCCCTACTCGGCACTGCTAGCGGGTCGACCTGGATAGCCGTAGCGCGAC.AGCGATTGTCTTGAGTGCTCGCCAGATCCTTCTGTCCTGTATTCATACA.AGTGGGAAAGGG 88!F8F#--!-8!FF8F!FF--FF-!!!--!F8F-!-!8F--!88FF!F-F---88-88-!-!!FF8!!-FF8!----!FF--888F!#F!88-8!-FF!F88FF8--8!-!8---!-888-F!8-8-F8-!88-FFF#-8-!!--F-88- BC:Z:AGCCCCCT-CGTNATTA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

15

</td>

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

13

</td>

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

<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">HiMom:1:1101:1127:1000       77      *       0       0       *       *       0       0       TTTTCTTTGTTA.GCCGTC.ATGGGTCC.GGCCCACCGTACA.ACCCATCAGCGTCTGACG.CCGTACTTCG.TACTTATGGTGACTGTGA.TGCCACGACTTGTCAT.TACTTGGGGTTGTGA.TA.TACACCCTATCCGAACTT.AGGT F8F-8!-!F8-8#!FFFF-#FF--F8!8#8!F-8-!!--8!-#-F-88!8-!FF!FF8F8F#F-FF8!88-8#--8!F-F8--F-!8F888#!!--8!F8888!F!8!#88-F88!!-F!F8!8#88#F-8F!-F!8!8!!8F-F8#88FF BC:Z:CACTTTTC-GTTGTAGG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

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

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

16

</td>

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

14

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">HiMom:1:1101:1127:1000       141     *       0       0       *       *       0       0       GCTTGCCATTT.CCGGACTCTATCCGTGCTCGTAGCACAC.TATCGGCACGCCTTC.ATACACTCTGACGAC.GGCCCCTATGGAATGA.T.GTCATCTACACCCTACTCATGAGATTTTAACGGGACAGTAGGCTACATCGGGTCAAACG F!888-FF!!!#--!F-F!F!88-F8!!!!-!---!8!F8#-8F!F-!FF!F-8-8#88F8-FFFFF-!--!#8F!F!-8F!F-F88F8#8#F88888--8-88!!F-8FF8-F!F!FFF-F-F888--8FFFFF--88-8-8--!FFF-- BC:Z:CACTTTTC-GTTGTAGG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">HiMom:1:1101:1145:1000       589     *       0       0       *       *       0       0       TTGTC.CCTT.GCTAAAGATCTCCGTCGCTCGTCTCCTG.CCCGTATCTACCTAAGCCT.CTGCG.GGTTCGTAGCCCGGCCTACAAGGCAGGCTTCA..T.TGCGG.GGGAC.GAAACGCCACGCTAACCGCTCAGGCAGTAGAGCTAGT !-8-F#!8--#FF8F-FF---!F!!!8-!!F88!!!--!#!8F88F!-!-F-8F-FFF!#FF!8-#!F-8!!!88F!!8!-!888F-!FF8F88-8!-##!#!!8!8#-!FF!#-F888!F-F--FFF88888F8F------FFF!!8-8! BC:Z:GTAGGGAT-AGCCGGCG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">HiMom:1:1101:1145:1000       653     *       0       0       *       *       0       0       TCACTCTTCATT.TGGTCTTGCTGAATCAGCTTATCTTGATGAGAGCG.CTCCTGACTGGGAGG.TGCCC.CCAGA.TAT.TGACCCCG.GACAGCTGTGAC.ATCAGGAGCC..TTCCGCTCCCCCG.AGTCATGTATCGCTTTAAAGAT !F8-F-8!F8-8#!!FF-!888F8888-888!F8!--8!FFF-F888-#8!!!-88-!-!!F!F#8F8!F#-F-!8#!8-#F8-!!8!-#F8---F8FFFFF#-F-F-F-8-!##--8!-F!!88FF8#88FF8-88F!888!!8-F8-88 BC:Z:GTAGGGAT-AGCCGGCG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

</td>

<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">HiMom:1:1101:1163:1000       77      *       0       0       *       *       0       0       TCCT.CA.TCGCACCGGAGAATTCCCACGATTCCCAAGC.AA.ACGATCTAATCTGAGCTTAGAACGAACAGACTCGGTAGGGGGATATTGTATCGCTGCCGTCGCGTGCTATGCTACGGTCTC.GTTATAATGGC.TTTTGGTCGCTTTA F8F8#-8#-8F88!F--88F8--!8!F8F8!!F!!FF-8#-F#FF--F!8888-F!--88-888-!F8F!8FF8--8!FF!888!8--F8F-F8F!-!8---88-F8F-!!F888-88F8!F88#F-FF8F-!!8-#!F!-!88-!F!888 BC:Z:TGTCTATT-CTGCGTAC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

</td>

<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">HiMom:1:1101:1163:1000       141     *       0       0       *       *       0       0       GG.GCGC.CTCCGCACGCCA.TAGCA.CTTG.GTAGGCCCTT.TTTCCAGTTTCTGGTAGGTCTCGAGGCGTATCGTTT.CGGCGTCTTTCCACTGAAAGGGGGTCTTAGGATGGTATCTGGT.GCG.ACGTGAGTGTATCGCACGTACCC F8#!8-!#8!8-8!88-!!-#8-!8F#8!!!#F!F--!!---#-!---8-!-FF!8!!F!8-8!!!F!--F!888!F--#F8F8-F8!F!-!8F8!-F--8!F!F8FFF!F-!!FF-FF88F8#---#8--FF-!!F!-F8!F888-FF!! BC:Z:TGTCTATT-CTGCGTAC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

</td>

<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">HiMom:1:1101:1181:1000       77      *       0       0       *       *       0       0       CGCGTGAAACGTCCACAATAG.GACGTCGCGTGATGTTGTTCTA.GGCGATAC.ACGAGGTGATCAGAAC.CCTTCAGTTTGTTGGAGTC.CTTCTGGACACC.CACCCGGATGATTAAGAGCTACGCGCTAGCCATATACGA.ATCC.TC !8-!88888-!F8!888F!8!#8--F!F!--!-F!-F-!8!F88#!-!----F#---F-8F!8!-8-8--#8-F!F88-!-!F8!!-!!F#8F--F8FF-8!-#-FF-FF8F!FF-!FF8-8---F!F8F888!!--FFF---#888!#!- BC:Z:TGTGTCAG-CTAGTCTC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); 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="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,8 +40,6 @@ HiMom:1:1101:1416:1000       77      *       0       0       *       *       0       0       AACTTGGGTGCCCGC..GCTCTCGAGGCT.G.ACGTCATG</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

</td>

<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">HiMom:1:1101:1416:1000       141     *       0       0       *       *       0       0       TGGTCCTCTGGTCAGCAGTTCTAAGTGCCGTCTATGG.TGGGT.CACCA.CGCTA.GT.ATAGGTCCCTAGGTCGGGCGTGCGACTCACCGCCGGAAGGGGTGGCCGGG.TATTTCTTCCAGGCAAGCCA.CTAATGGTAAATCTGTCGCA -8F8F-!-!--F!F8-F-!F888FF-F--F8!--888#888!!#-F-!-#F-8!F#!!#----!8-!!88F8!!F8-888!FF8!!88!8FF8!---F!F88!8-8F88#-F----F--8F-!FFF!F8-#-!-F!F88--8--!-8-F8- BC:Z:TAGCGTTN-ANCGGGCT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

</td>

<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">HiMom:1:1101:1434:1000       77      *       0       0       *       *       0       0       TACTC.GTGGACTTGTATCC.GGACTTTCTCTCTG.TACTGGGTT.CGCCGAACTCCCCGTT.AGCCATC.CGGTGCTGGACCACA.ATCGCGTC.GACATGCGCACTAG.CGAACCCTATACTCTA.TTC.CCTTCGCTTCGGCAGTTGT -888!#8FFF-F!-8!F!F-#!8-F888F8-8F!8#!FF!!8-!-#-8F!!8F8-F88!-F!#-!8-88!#-F8F88!F8-!F-F8#F!F!F!--#8-8-!F8!8-F-F-#FF8F-F8!-!88-!8F#!!8#88-8!F!!8F8!-F88!FF BC:Z:AATTTGCG-AGCAGNGT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

</td>

<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">HiMom:1:1101:1434:1000       141     *       0       0       *       *       0       0       TTTGTTTCAGGGCCTTTGCCGT.CGCA.TATTGTGTCTCTTCCCAGCAGCTGTCCTTAATGAT.TAGCAGATCGCCTGTGCATTA.CGCACCTC.TCGTA.AGGGGTGTTCCAACGCATACA.CTGC.TGG.CGT..CAATGAATCAGATT --!!F!8!FF-!-!88!88!-!#8-FF#F888F!!F!8--8F-!FF8-!F-8FF!FF8F8!88#8--!888!-F!FF8F8F-F-F#!F!88F-F#8!!F8#-!8!---88!--88F-F-88F#8888#-F!#FF!##!F8-!-8F8F-8F- BC:Z:AATTTGCG-AGCAGNGT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

</td>

<td class="diff-line-num new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">HiMom:1:1101:1452:1000       589     *       0       0       *       *       0       0       T.GGGCGCAGTCCGGGGTTAAA.CAGTTAGTCGGCGTCGCCTAACAAGCTCTTGAGCCATTGCGGCTT.TTATGATGCCTCAATTGTTGGGCCTGTGAGACCGGGGCG.GGGCCGCAAAGGCG.C.TAGTCTC.GAATTACAACCCTG.CG -#FF!8!8F-8!FF8-F8!--8#F88FF-FF8888!!8!-8!-F8FFF8-!F88FF-F8-!!-!-F8F#!-8-!-F-!F!8FFF8!!8F!!-!!FFF-!F!!8!F8!F#F--!F8--888888#!#-8--!-F#-888-8!------F#8! BC:Z:TCGGCAAC-CCNATNCT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

</td>

<td class="diff-line-num new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">HiMom:1:1101:1452:1000       653     *       0       0       *       *       0       0       AAGATCAATTTATGCACGGCCACTAGTGTGGTGAACACCTGT.GTAGTACTTGGTTTACGTCTCC.CTATCGTGCCGTAGAGTTCCCTGTTGGTATGTTATAGGGAACGGAGCATCTCATGCGCCAAACGAGTTTGACG.TGGAGCC.GTC -8-FFF888F--F8--!8-!--!8F-FF--88F8FF-8-!!F#!-8-!88FF!F--FF!!F8-88#!-F-8---!!F8888!FF!F8!!!8---F88F8888FF!-F--F8-8F-!8FF--FF-888F-F8F-F-8-F-#!FF-8!8#!8! BC:Z:TCGGCAAC-CCNATNCT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

</td>

<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">HiMom:1:1101:1470:1000       77      *       0       0       *       *       0       0       .ATCTTTGGGATCATGAATTAAGGATTGTCCATGCGACAAGC.ATGTAC.ACAGCG.ACAGAATTG.TACGATGAACGTCGTAGTTGCGTTACCAAGGCACTAG.ATTACCCTCT.GGCCTCGATTCG.CCACCCTCTTGG.GGTCCCGAG #---FF8F888-F8-8F-!8F88F88FFF-FFF-!8F!F-!!#-88F--#F8888-#F8F!FF8--#!-8F88-8FFF!F8-F!F8-FF!88--F-F888-8--#8F88--FF8F#88-8-F!-F8-F#F8-!8F!F--F8#-F8!8-8F8 BC:Z:GANCGAAC-AGNTGGCN  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num 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">

50

</td>

<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">HiMom:1:1101:1470:1000       141     *       0       0       *       *       0       0       GGGAATTCCGGTTTTTGGCGAAGTCTCGATAACTTCCGCGCGGCACCTAACTTGCCAGCTGTGGTTCGCGTCGTGA.TTAATGTTGGG.TCTCGC.CGACATAAAA.TGTAAAGGGAGGCCTTGGAGGCCC.GGTGTATGCT.CCAGCTGG --!-8F-88F-F---!8!F--8FF!8F--!---!-888--8F-F--!8FF!8-FF!8-!8-!----8-!8-88FFF#8!-8!-!-F!8#-8-!!-#8F888F8FF8#--!888!8F8!F888!!-F8-!-!#F-888F!8!-#F!F8F8!F BC:Z:GANCGAAC-AGNTGGCN  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

51

</td>

<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">HiMom:1:1101:1488:1000       77      *       0       0       *       *       0       0       GGTCCTGTTTATGCGTTCGCTGA.G.TGA.ATCACTGCCGGATGGCTT.ATAGGTTG.GT.ATCTTACTGCGGGGCACTCAAGTTCCGCCCAAGCA.GATTGGATTAAT.CAGAA..ATG.CGGT.CCGCG.GCC.TGTT.AATTTCATCT --!F-!FF-F-8FF!!F!F!--8#8#FFF#F!!8!F88-!F8FF!-!-#-!8!F!--#!-#8-----!F8!!!F88F-F8F-8FF8!F!8---FF-#--F-FFF-8-8F#FF88-##88-#FF8F#F----#-FF#8!--#-F-F8FF88F BC:Z:CGTCNTGT-CTTCCTCA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -56,8 +50,6 @@ HiMom:1:1102:1018:1000       77      *       0       0       *       *       0       0       .GGAAA.GGATAA.CCAGACACCCAA.GGATATGTAGCAT</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

56

</td>

<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">HiMom:1:1102:1018:1000       141     *       0       0       *       *       0       0       TTTCACCAGGCCTCCTCGTAAGTAGATCTTATTTGGATCCAGGTAGCATCGGGGGAGCCGACATT.GTCC.GTCTCAGCGTCGTCCACCTACTCTGACG.GTACCAGAGTGCTCCCGGTACCTCAGTGCCAAGTCGGATTAGCTTGCCAGT 88!!8-8F-F-F-8-!!-!F88F-F-8!FF-8F!8!F!8FF-FF88-F8!F!!8-F!F8FF8FFF#!8!F#8888!-8-!!F-F!F-F8!-!88!--F-#!F88!F!-!F!8-8F!!-!F!--F--F8-!8888F!!8F88!!----!888 BC:Z:TCGTNTTG-CGTGGATT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

57

</td>

<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

51

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">HiMom:1:1102:1036:1000       77      *       0       0       *       *       0       0       CAGTGTTTGTTCGAATCCGCTCCCTTCTGCTGACGTGGGT....GG.AACCGAAACGCTTTTCTCCCAC.CCGG.GTCGTTCAACTCTA.ATGGGACAGCGCATGGTTCGTCTA.GC.TGACTCGTGGCA.ACGTCCTACGACCGCTAAAT F-!8--!F-F-8!F8F888!!!F8!F-8F!!F-F-F!-!F####!!#-FF8!F-F!8FF--8F-8FF-!#!--F#FF-!8FFF---F!-#8-F!!8!--F!FF8-88FF8--88#F-#!!-FF!F---!F#8F--88!F-!--!8!8F8-8 BC:Z:NCATATCT-ANAGGCCG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

</td>

<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

52

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">HiMom:1:1102:1036:1000       141     *       0       0       *       *       0       0       TTCCTCG.ACGTCTTTG.AGA.TTTCGCCCAAGGCTTGTCC.TGCAAGACGTCCTGTCGTATAAAC.GCCACGGGCGGCTAGGACTTGGA.ACGGACCT.ATAGTTCCTGTGCCACTT.TCG.GTTTTCGTCTTGTTG.TGCGA.AGGGG. F-!--F-#-8-F!-F--#-!-#88888F-FFF-F!8F!--!#-!-88-F!!F8!88-8-!8--F88#-F--F8FF!-F!!8F8FF8FF-F#--F-F8-F#F-F!F!!FF8!!F!88!F#!-!#-!--F8--!-8!8-8#F88-F#-8-F-# BC:Z:NCATATCT-ANAGGCCG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

59

</td>

<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">HiMom:1:1102:1054:1000       589     *       0       0       *       *       0       0       CGGG.CCGCCAGAT.TTCCCCGTTCCCACGGACGTTCCTTGGCAGCGCTACTGTCGGGGTTGATCATGCCGGTGTAGCAGGCGT.CCGGACAGTGAACTAA.GTCTTGATTCCACCG..CATAGC.TCTGATACACCTCAATTCGAGTTCA --8-#-8F8FF-FF#--F8!--8--F8F!!F88F-!!F8!!8--F8F888F8F!--8!88F-F88--!F88-F!--FF-8-FF!#F!-88F-8FFFF-!-F#-F8!-!8!!-88!F-##!F-88!#F-F---FF8FF8!8F-8F-F!-8!8 BC:Z:CTTATTTA-GGCTNTAG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

60

</td>

<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">HiMom:1:1102:1054:1000       653     *       0       0       *       *       0       0       G.GAGTAAC.GGATTCGCCAGTAGTTGTTGCACTTGAA.CTAACGCCATTTCGTCCACGG.TTTCTTCGAG.CGGAGGCCGTGGTCCC..CGCGCAGAT.GTT..GAAGTACCGAGACTGGCCGTGACACTGCAC..CGGGA.ACCTCCGC !#-8F88--#88-F8!--F8---!FF8!!FF8F8-FFF#88F8FF!!-!F!-FF!8F-8!#!8!!-!!--!#F8F-8FF!!F!-88--##!F!888F-!#-F!##!F-!--F!F8!F-F8F8FF!FFF888!88!##888-8#-!-!8F-F BC:Z:CTTATTTA-GGCTNTAG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

</td>

<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

53

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">HiMom:1:1102:1072:1000       77      *       0       0       *       *       0       0       GCGCTTGTTCCGATTTGT.TGGCGCTGCGGCAGCCTGATCGG.GCGCCTTGGT.GAGAGGCGCACTTGCACTA.CG.CGGGCTACCGCCA.ACGTTTTCTCTGCCGG.AGCCGTATCCGGTTGGAT.TTCCG.CCATCCACGAACTTCATC F---F!!-!8!F8F8--F#8F-8888!!--F8!-88-F88FF#!88F-F-FF-#FF-F-FF!-F-!FF!8--F#-!#F8FF-F8!FFF!-#F!F8F8!8FFF8!-88#--8!FF8F-8!F8-!8-F#8-!--#FF8!!--!!FF8FFF8!- BC:Z:CCCATGCC-GATGTTTA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

</td>

<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">HiMom:1:1102:1072:1000       141     *       0       0       *       *       0       0       A.GAGGC.CCGCCCC..TT.CTCGT.GCCCTCCCAACCGTGCGACTGG..GCGCTGGACATCGTCGCAACTTACGGCGTGTGCCCTGAAGGTGACTACACCG.TGAAAGG.CGCCTCGCCGTCCATGCCACAAGGTGGACG.TCATCG.CT 8#--8F-#F8!F!F8##88#-!F-8#F!-F---FF-F8-!8-8-8F8!##--F-F-8FF-FFFF--8--!8--F--!FF!!-!888FFFF!!!-!--F-8!-#--8FF!-#FF-!8F!-F-!-!8-888FFFF-8!--8!!#-F-8F!#!8 BC:Z:CCCATGCC-GATGTTTA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

</td>

<td class="diff-line-num new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

55

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">HiMom:1:1102:1090:1000       77      *       0       0       *       *       0       0       GCCTACGCATCCGCCC.CACTG.ATGGGTGAGCC.G.ACTAAGCTGTAGTGCCTGATCCCTCCAGGAGCCCTTTA.TGAATCGGAACGCTATGCGACTTGTGATAACGAAAATTTCAGAAGTT.ATCGCCAGTGTGGTTCTTCC.AACATG !-F-88F88!!8!--8#---8!#F8F8-!F--8!#8#8-8F-8-!-F888FF8!8F88!-F-F8!8F---!F8!-#8F-F8!F--8F!!!8-F8F8FFF!!!---8!-8FF8F!-8-!FF!F-#-FFF88-8!!8!!8-8!F-!#FF!8!- BC:Z:TTGCCTTT-TTTCGGTA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); 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="58" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -66,8 +58,6 @@ HiMom:1:1102:1108:1000       77      *       0       0       *       *       0       0       TTA.GGGGAGTGC.AAGG.CTTA.AGTTCACCGAGCCCAT</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

</td>

<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

58

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">HiMom:1:1102:1108:1000       141     *       0       0       *       *       0       0       TTTTCCAGTC.TTCTTGCAGGCCGGTGCATCGGCTT.ACGCAATG.CCCCTC.ACGTTGTGAGTGTCCCGATCAATTTG.GC..AAGTACCAAAGGTGCCTGTCTGTAGTTGAACATTACGTGGCGTATGG.GTAAGTTTCTATGCACGCG 8FF-8F8-88#F8--8F!F--8888F-8F!!--!8-#8-8-8--8#8-8F!F#8!F-F-8!--!8-!!8!88!-F!!8-#--##F--8-!-8-F!FFFF88!8-8FFF-!F8FF8FF-F!--F88-!-!!8#-F88!F8F!8-F-8-F--- BC:Z:CCCGNGCT-CATCCNTG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

</td>

<td class="diff-line-num new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

59

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">HiMom:1:1102:1127:1000       77      *       0       0       *       *       0       0       GCC.AACGATCTT.TTTGCTC..CGTG.TGCTTGGTCTTCTTGTCTCTAACTA.CGTGTAGTGAGAGT.TCTCTCTCGAGCGT.TCTGGATTGC.CGACGGACGAGGAATTAGTGCTCAGTGTATCGGACC.TTTTCTGGCCGCATGCAGC 8!-#8-8!-F!-8#!8-!88-##8-FF#FFFFFF!!F-F-F-FF!F--8-8-8#!!!!!88-!F-F-!#8---88!FF8-FF-#-!8-!88-8!#!8--F-FF8FF88F!F8F8!!8!-F!88-!!-F8!F#!8---!-!F!--8--!F!8 BC:Z:GTGGCAGA-GAAACGAA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

</td>

<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">HiMom:1:1102:1127:1000       141     *       0       0       *       *       0       0       CGCCGCTATTCCGGACA.AT.GTGTGACGCTTTCCGTCTCCCGTCGTCTCGATTTGGCGCC.ATC.TCCGTCAGCCTAGAG.A.TAACGAA.CTGGATGCTGC.CATTGGA.ATGACTACCTGCTACTTGG.ACGATTCTGCACGTCGTCT !88F8FFF!8888!-8-#F8#-8!!F-!FFF!888--8FF-F-F--8-!FF8-F888-F!8#F--#!88!!-F-FF!F-8-#-#!--FFF-#8-8-8-!-!-!#88F!!8F#F!8FFF8-F---FF!-888#F8FF8------88--8F!- BC:Z:GTGGCAGA-GAAACGAA  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

69

</td>

<td class="diff-line-num new_line old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">HiMom:1:1102:1145:1000       589     *       0       0       *       *       0       0       AGATTTGTCAGAGTGT.T.TCAGCGGTA.CGTAGTAGGCGGTGTTGGGCCGGTTC.T.TA.TG.TCGAGCAAG..ACGGGCACACTG.CCATT.ATCCT.ATGCAAAAGC.TGG.CCC.TGGGAGGAGCCTAGCGAGCGGGGGCGTTTTTA 8-F-8FF88F!-!F!F#!#!-F-8F!!-#8F888-F!8!8!!8!888-!F!FF!-#F#8-#!F#F-!88-8F!##-F--!--FF-8F#!8FF8#--FF-#8F!-FFFF!8#8!F#-!-#8-FFF!8-FF!8-8--FF!-!8-!!F!!-8-- BC:Z:GGTAAGGT-TCCACGTT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

70

</td>

<td class="diff-line-num new_line old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">HiMom:1:1102:1145:1000       653     *       0       0       *       *       0       0       ATAGATCCTGTTTAGCCGTTGTTGTTAGCCCC.TCTAGC..ATACCGAATC.GCCCT.CGATCTCCTCAGAGTTCGACCTTCCTTTC.GGAGAGGGTACCTCTCAGAA.GCAAGGATGCCCATGTCACTCAGATCCTA.AT.AGAATCTTT 8-F8F-!-!F8F-F!!8--!8F8-F-8!-8!!#88-8F!##F-FF!!FF-8#F--8F#-!FF!F-FF8-F8!-!--F8!8!!88F8-#!!F!-F-88F888--8F!FF#---FF8F8-8!!-F!F!8!-F8-8!-F8-#F!#-FFF!-F-F BC:Z:GGTAAGGT-TCCACGTT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

71

</td>

<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">HiMom:1:1102:1163:1000       77      *       0       0       *       *       0       0       GATACGGTGTTATTCTTCTTGATTTGACTACG.GTCCGACAAC.TATTCGTGGAAACACGGCCCAATAGCGCT.GCCC.ACAGCTTTATAGTGTCA.CAGTGATTACGTCG.TGTCAGGGTTTACAATG.AG.GCAAGCGTTTGGCGGCGA !-!888F-8!!8!8--88!888---!8FF88F#--!F8-!-F8#F88F!88!!F-8F8-8!--!-F!FF!8-F#F!!8#-!F88F-!-FF!8FFFF#F-88F8F!8!!8FF#!8-!F888F8F--FF8-#88#-!--F88F!-F-!--!F- BC:Z:CCGCGCNC-NGGGATAT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

</td>

<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">HiMom:1:1102:1163:1000       141     *       0       0       *       *       0       0       CCTGCTCCTCGGCCGACCTG.CCCTAATGCAGTTGCTCCGGA.CTGCCAACGAAAACCTTACTC.TCTA.CTCGTA.ACTACGGCACTGAAGCA.TC.GCCC.TTTGTTC.CGTCTAACCACTCTTTCTTCGCGCGAT.TAAGGCCT.CTC F!-!-F88FF-!F-88F!-!#-8!8-F!88--8F!!FF--8F#-FF88FF---F8F8!88F8!-#F!!8#88!-FF#-!FF8!F-F!88F----#!-#-!F-#8!--!!8#88FFF88F8-8!!-!F888!!FF!8F8#8-F!!!-8#F!- BC:Z:CCGCGCNC-NGGGATAT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

</td>

<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">HiMom:1:1102:1181:1000       77      *       0       0       *       *       0       0       TAGCATCGTAAACGGGACTTCGCTAGTCCAGTCTCTTACTAGTCCGG.T.TGGACTA..GTT.TGTA.ACCCGACTCGGA.T.CATTAGTCAC.CAGACT.CTGT.G.CATCAA.GACCC.AC.CCTCCTTCCCAGATAACCGTT.GTTTC -F!!8F!F!F--!F-F--F!-!---8F!!F-FF-!F8F8F--F--8-#-#-8!F!!F##-88#-8F8#-!-8F--!-!!8#8#8-!F88-8--#-F--!-#!---#-#F-8FFF#8888F#8!#F-888!!!-FF-F!FFF!!!F#8!F88 BC:Z:CGCGTAGT-ATTCCGAC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,8 +88,6 @@ HiMom:1:1102:1416:1000       77      *       0       0       *       *       0       0       TGACTACTTAGTAACGG.G.CCGTGGCCGCTACTGCGCCG</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

</td>

<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">HiMom:1:1102:1416:1000       141     *       0       0       *       *       0       0       TCGGCACGACTACTAGTAGCAC.CCGCCTGGGTCAC.TAGCCTCAGTTGGCTCAAATTTGGCTGGAATGACTAATCATATTTTGTCCATACAATCGATCTTTGGGCCTCCC.CCCCAT.A.CCGCGGGGTACCTTGTGCCTCTCACTTGCC -8!FF8!!8F8F8F-!!F8-8F#FF88!8-!!!FF-#-F8FF8F-FF-F-8-!8FF88!8-88-88F!-F!F888888-!!F8F!!FFFFF---!FF!-!F88--8---!F#-!8FF!#F#!-8!--!FF-!!F88!8FF--!88F88F!! BC:Z:TTAGCGTG-GTGCCAAG  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

</td>

<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">HiMom:1:1102:1434:1000       77      *       0       0       *       *       0       0       CGGGGACAGTGTCATTATCGCC.CCG.GCAGG.TTAAG.C.T.CCGG.GGGGGCAGTGCTATTCCGATGTCCCCG.AATAGTC.TGGGTCAGTACCCATGCCCCTTATA.AGC.ATAT.GTAG.CAGCGGCTTGCGGCTCAGCCCATTTTA -8-8---F!8!-8-!!FF8!!-#8!-#8F-F8#F--8F#-#8#FF8F#-8FFF8-!8-!-8FF!-!-88F88!-!#8F8F-FF#!!-F888-F-!-888!FF!8FF8F-#88!#888!#8FF8#!888!-88!!8--8!!-8-FF-88!8F BC:Z:TNNGAGAA-TTACGCGC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

</td>

<td class="diff-line-num new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

90

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">HiMom:1:1102:1434:1000       141     *       0       0       *       *       0       0       CCCTATTGCACTTAG.GCGTGGAATCGCGGGATT.CGGCCCCCG.CAGTCGGCTATGATTCGA.TCCATGCGTGCGTGTGTGCGTATCCCCACGTATAAGAGCGCGGACACTCCA.CTGGGAACCAATC.CA.TGAC.TAGCCGACAATAT -8F-F8!F-F8-888#F8FF!!F8F!-8!8!8F-#8F!--8F!F#-8!F!8!-F8-!8F-FF-#-8--8!!88-----F-8--!!888!-F8!-88-----!8!88!8-8-!!-F#!--8!8-!!8--F#!-#F!--#F-F!-!-!F-F88 BC:Z:TNNGAGAA-TTACGCGC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

101

</td>

<td class="diff-line-num new_line old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">HiMom:1:1102:1452:1000      589     *       0       0       *       *       0       0       GTTCCGGACGAAGGACTGGATTGCTGCTCAGAGATCCCGGTTCCAGGGTCGGT.CAATTTGTCCGCCAGGTGGA.CTTGTTCTTTCAGACTAAGGTT..AGTGA.GCCAGCATTAAGATACAGAAACAACTCGTCCCCT.TCTGACGATCA 8-FF8!---FF8!!8!-F!8F!8--FF-8F!F!F!!!F-!8F!-8F8F!8!88#FF-88FF!-!-8!F8-!!--#!!-FFF-F8F8--8-F--8!-!##-F!8F#-88F8F-!F-F8F!8-8-FFF8FF-8F-!88!8!#-8F8-8F---F BC:Z:GGGGCACT-GGCCCGCT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

102

</td>

<td class="diff-line-num new_line old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">HiMom:1:1102:1452:1000      653     *       0       0       *       *       0       0       GCG.CGCTTCG.G.CCGGATGACCTGCTTTGTT.CTCAGTTTTTTTTATG.T.GTACATTCTTCCCTCGATCGAGTGTGTTTGCCTGCGGCTTAGTCGTGGGCTCGCG.CTGT.CGAGGCTGTCATTCCAGGCCTGCCAA..CGGCGGTCT !-F#-8!-F!!#-#-!!F-88--!F8F88F--!#FF-8!8!-F8F--8F-#!#8888FF!F!!-F!F!--!!--!88F!8!8!F-!FF!F8!-FF-88-F-!F8-!F-#-8F!#FF888!!!-88-F!!F!-FF8!!F--##8F!---F!F BC:Z:GGGGCACT-GGCCCGCT  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

103

</td>

<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">HiMom:1:1102:1470:1000       77      *       0       0       *       *       0       0       CAGACCGCGGCTCTGGATCACCTCCGACGGGTAGTGACA.CTACCT.AATCCGTCCAAGCAATGTGCAGTTCTTAATGACTTGGCTCGAGTAGTCCTGACCAA.GAACGGACGTTCTTCGA.GATAGGTGGGAG.TGGCTTCACGCTTTAC 8FF8-FFF!F-8--F-888-!!-!-8--8FFFF!!F8FF#!!F!!8#F8!8F8-8-8-F!--8-F!8----!F----8-8-F!!-F!F-!F-!!F-F!FFFFF#F--F----!!F-!!F--#88!F!F!8-F--#-F8-F-!-!!-!!!-F BC:Z:GGGCAAAT-CTGGTNNN  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

</td>

<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">HiMom:1:1102:1470:1000       141     *       0       0       *       *       0       0       AAGCAA.GA.GACACCGGTGTCAGTGTTTTGG.ATCGCAGCTTT.GACCTGCTTCCT.AACTT.TCTGTTTCCGAAGTCACTTATT.TAAACGAGCTCTGGACTAGGCTCTGTACTCCCAATCTCGT..TCTCGGGTCAA.GAGCCTGGCC F8-888#!8#-8--F--!F--888!8F8!-F8#-F!!!--!F8-#--8--F-!8FFF#--F!-#!F-!!!F-8-FF8--F!-88!8#88-F-F-8F--!8!F!-8-F--!88FF!-8!--8-!88F!##-!8-!!FF8-F#8FF-!!!--- BC:Z:GGGCAAAT-CTGGTNNN  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

105

</td>

<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">HiMom:1:1102:1488:1000       77      *       0       0       *       *       0       0       CGCTGTGCGTAACTTCCATGAATATCGAGGTGGATCTC.GTAGTGTTTG.AC.ATAGGTACAAACGTCCAACATGTCACGTCGAGAACGCCCCGATGTGCGCGAGAAGT.ATGAGCGTATGCAGGGCGTCAATTGCCCTTGAGAAGGTGGG FF--8F88!!-8-F8!-FF!88F-!F8F!F!!F--F88#!88-F-F--F#8-#8-8-8-8!F-88!8!!FF88!FF!-8FFF--8-8F8-FF8--8FFFFF-FFF8888#F8!F!888-F!--!88-8!---FFF-!!F!FF--8F88-!! BC:Z:CTCATACG-CTGNTCCC  RG:Z:HiMom.1</span>

</pre>

</td>

</tr>

</table>

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