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<h3>
Dylan Aïssi pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/beagle">Debian Med / beagle</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1">19dc4045</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-03-27T09:31:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.1-200324+dfsg</pre>
</li>
</ul>
<h4>9 changed files:</h4>
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<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
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<li class="file-stats">
<a href="#deffeee20209b899ad68dc536a5f9f142ada4d5e">
phase/HapImputer.java
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<li class="file-stats">
<a href="#8d85139a044149b6a2dee62e1ed355e1a107e93a">
phase/HmmUpdater.java
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<li class="file-stats">
<a href="#bff5675255d46d340fc57b49cdb9d933b6ba9ad4">
phase/Ibs2.java
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<li class="file-stats">
<a href="#55b6fb2cf31c47611bc2ebee66d816160c3223ae">
phase/ImputeBaum.java
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<li class="file-stats">
<a href="#d0875a14cecab64969d49fa0ec30b89961d311ed">
phase/PhaseLS.java
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<li class="file-stats">
<a href="#1ac54fb4d23beda1b68dc539cae4477660958812">
phase/RecombRegress.java
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<li class="file-stats">
<a href="#6ba560a119d50b4bdbe6c09549cb4a9204ac0f16">
vcf/PlinkGenMap.java
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<li class="file-stats">
<a href="#ec6a94af868b7dfb86724b44ca474651fa26375a">
vcf/RefIt.java
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<h4>Changes:</h4>
<li id="2ad0efaccf66628e1858a4c133e8914e33eb2221">
<a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1#2ad0efaccf66628e1858a4c133e8914e33eb2221"><strong>main/Main.java</strong></a>
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<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">@@ -65,8 +65,8 @@ public class Main {</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The program name and version.</span></span>
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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="LC66" 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="LC67" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"(version 5.1)"</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="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.2<span class="idiff left right">5Nov19.28d</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.2<span class="idiff left right">5Nov19.28d</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.2<span class="idiff left right">4Mar20.5f5</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.2<span class="idiff left right">4Mar20.5f5</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC71" 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="LC72" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The copyright string.</span></span>
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<td class="diff-line-num unfold js-unfold old_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="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">@@ -78,7 +78,7 @@ public class Main {</td>
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<pre style="margin: 0;"> <span id="LC78" 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="LC79" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">SHORT_HELP</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">PROGRAM</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="no" style="color: #008080;">VERSION</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 class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">COPYRIGHT</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Enter \"java -jar beagle.2<span class="idiff left right">5Nov19.28d</span>.jar\" to "</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Enter \"java -jar beagle.2<span class="idiff left right">4Mar20.5f5</span>.jar\" to "</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"list command line argument"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Par</span> <span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1#deffeee20209b899ad68dc536a5f9f142ada4d5e"><strong>phase/HapImputer.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">@@ -42,9 +42,9 @@ import vcf.Samples;</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="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">HapImputer</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Markers</span> <span class="n" style="color: #333;">markers</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Samples</span> <span class="n" style="color: #333;"><span class="idiff left right">s</span>amples</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="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;">nHaps</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicReferenceArray</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">LongArray</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;"><span class="idiff left right">h</span>aps</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Samples</span> <span class="n" style="color: #333;"><span class="idiff left right">targS</span>amples</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="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;">n<span class="idiff left right">Targ</span>Haps</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicReferenceArray</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">LongArray</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;"><span class="idiff left right">targH</span>aps</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicReferenceArray</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">PartlyImputedAllele</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,11 +56,11 @@ public class HapImputer {</td>
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<pre style="margin: 0;"> <span id="LC56" 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="LC57" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">HapImputer</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Markers</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Samples</span> <span class="n" style="color: #333;">samples</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="LC58" 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: #008080;">markers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left right">s</span>amples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nHaps</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;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left">haps</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">AtomicReferenceArray</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><>(</span></span><span class="n" style="color: #333;"><span class="idiff right">n</span>Haps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicReferenceArray</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">nHaps</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="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;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nHaps</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" 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: #008080;"><span class="idiff left right">targS</span>amples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">n<span class="idiff left right">Targ</span>Haps</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;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left">targHaps</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">AtomicReferenceArray</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><>(</span></span><span class="n" style="color: #333;"><span class="idiff right">nTarg</span>Haps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicReferenceArray</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">n<span class="idiff left right">Targ</span>Haps</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="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;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n<span class="idiff left right">Targ</span>Haps</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"> <span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>(</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,7 +70,7 @@ public class HapImputer {</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the list of target samples</span></span>
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<pre style="margin: 0;"> <span id="LC71" 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="LC72" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">Samples</span> <span class="nf" style="color: #900; font-weight: 600;">targSamples</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">s</span>amples</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">targS</span>amples</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>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,7 +92,7 @@ public class HapImputer {</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws NullPointerException if {@code alleles == null}</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;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC94" 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;">setHap</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;">hap</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;">alleles</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="LC95" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">h</span>aps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hap</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allelesToBits</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">alleles</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">targH</span>aps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hap</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allelesToBits</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">alleles</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java"></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;">/**</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">@@ -137,16 +137,16 @@ public class HapImputer {</td>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code (0 <= h && h <= 2 * this.targSamples().nSamples())}</span></span>
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<pre style="margin: 0;"> <span id="LC138" 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="LC139" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="no" style="color: #008080;">GT</span> <span class="nf" style="color: #900; font-weight: 600;">imputedHaps</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="LC140" class="line" lang="java"> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">oldGT</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HapsGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">samples</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">h</span>aps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">LongArray</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">newHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">IntStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">range</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;">nHaps</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java"> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">oldGT</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HapsGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">targSamples</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">targH</span>aps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">LongArray</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">newHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">IntStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">range</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;">n<span class="idiff left right">Targ</span>Haps</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parallel</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mapToObj</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">imputeHap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">oldGT</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">LongArray</span><span class="o" style="font-weight: 600;">[]::</span><span class="k" style="font-weight: 600;">new</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC145" 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;">HapsGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left right">s</span>amples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newHaps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC145" 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;">HapsGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left right">targS</span>amples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">newHaps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">LongArray</span> <span class="nf" style="color: #900; font-weight: 600;">imputeHap</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;">h</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">oldGT</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="LC149" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">LongArray</span> <span class="n" style="color: #333;">oldHap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">h</span>aps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</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 class="nc" style="color: #458; font-weight: 600;">LongArray</span> <span class="n" style="color: #333;">oldHap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">targH</span>aps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">);</span></span>
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">PartlyImputedAllele</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">partlyImputedAlleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC151" 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;">partlyImputedAlleles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isEmpty</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="LC152" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">oldHap</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="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">...</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">@@ -165,15 +165,15 @@ public class HapImputer {</td>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC166" 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;">marker</span><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="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;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">alProbs</span><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="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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;"><span class="idiff left right">ref</span>Haps</span><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="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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;"><span class="idiff left right">targ</span>Haps</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="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;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">stateProbs</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nf" style="color: #900; font-weight: 600;">PartlyImputedAllele</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Markers</span> <span class="n" style="color: #333;">markers</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;">marker</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="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">alProbs</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;"><span class="idiff left right">ref</span>Haps</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">FloatList</span> <span class="n" style="color: #333;">stateProbs</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">alProbs</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;"><span class="idiff left right">targ</span>Haps</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">FloatList</span> <span class="n" style="color: #333;">stateProbs</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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173
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nAlleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">nAlleles</span><span class="o" style="font-weight: 600;">();</span></span>
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174
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">;</span></span>
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175
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175
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<pre style="margin: 0;"> <span id="LC175" 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: #008080;">alProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copyOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">alProbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nAlleles</span><span class="o" style="font-weight: 600;">);</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" 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: #008080;"><span class="idiff left">refHaps</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">ref</span>Haps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">();</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" 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: #008080;"><span class="idiff left">targHaps</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">targ</span>Haps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">();</span></span>
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177
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<pre style="margin: 0;"> <span id="LC177" 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: #008080;">stateProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stateProbs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">();</span></span>
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178
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178
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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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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -184,8 +184,8 @@ public class HapImputer {</td>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" 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="nf" style="color: #900; font-weight: 600;">imputeAllele</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">phasedGT</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">phasedGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isPhased</span><span class="o" style="font-weight: 600;">();</span></span>
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186
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">updatedProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alProbs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clone</span><span class="o" style="font-weight: 600;">();</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" 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;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">ref</span>Haps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phasedGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ref</span>Haps</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">+<span id="LC187" 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;">j</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">targ</span>Haps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phasedGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left right">targ</span>Haps</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]);</span></span>
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="java"> <span class="n" style="color: #333;">updatedProbs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">stateProbs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">];</span></span>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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191
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">imputedAllele</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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<a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1#8d85139a044149b6a2dee62e1ed355e1a107e93a"><strong>phase/HmmUpdater.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">@@ -90,4 +90,57 @@ public class HmmUpdater {</td>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"> <span class="n" style="color: #333;">bwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="o" style="font-weight: 600;">;</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC94" 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="LC95" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Updates the forward values and returns the sum of the updated forward</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * values.</span></span>
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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 fwd the array of forward values that will be updated</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 pSwitch the probability of jumping to a random state</span></span>
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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 sum the sum of forward values in the specified array</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 mismatch the number of allele mismatches (0 or 1) for</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * each HMM state</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param nStates the number of states</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the sum of the updated forward values</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException if</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code fwd.length < nStates || mismatch.length < nStates}</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws NullPointerException if</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code fwd == null || mismatch == null}</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">fwdUpdate</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;">fwd</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pSwitch</span><span class="o" style="font-weight: 600;">,</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mismatch</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;">nStates</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pSwitch</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pSwitch</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>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="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;">k</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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="java"> <span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pMismatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mismatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]]*(</span><span class="n" style="color: #333;">scale</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="o" style="font-weight: 600;">);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="java"> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">];</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="java"></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Updates the backward values.</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param bwd the array of backward values that will be updated</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param pSwitch the probability of jumping to a random state</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param mismatch the number of allele mismatches (0 or 1) for</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * each HMM state</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param nStates the number of states</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException if</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code bwd.length < nStates || mismatch.length < nStates}</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws NullPointerException if</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code bwd == null || mismatch == null}</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" 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;">bwdUpdate</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;">bwd</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pSwitch</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;">mismatch</span><span class="o" style="font-weight: 600;">,</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" 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;">k</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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="java"> <span class="n" style="color: #333;">bwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">pMismatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mismatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]];</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" 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;">bwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">];</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pSwitch</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pSwitch</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>
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142
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<pre style="margin: 0;">+<span id="LC142" 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;">k</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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</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="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="n" style="color: #333;">bwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scale</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="o" style="font-weight: 600;">;</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1#bff5675255d46d340fc57b49cdb9d933b6ba9ad4"><strong>phase/Ibs2.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">@@ -44,7 +44,8 @@ import vcf.RefGT;</td>
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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="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Ibs2</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>
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<pre style="margin: 0;"> <span id="LC46" 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="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MIN_STEP_MARKERS</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>
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<pre style="margin: 0;">-<span id="LC47" 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="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_STEP_MARKERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1500</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// value for high-frequency markers</span></span>
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<pre style="margin: 0;">+<span id="LC47" 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="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_STEP_MARKERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1500</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// high-frequency markers</span></span>
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<pre style="margin: 0;">+<span id="LC48" 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="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">MAX_MISS_PROP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.1f</span><span class="o" style="font-weight: 600;">;</span></span>
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48
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<pre style="margin: 0;"> <span id="LC49" 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="kt" style="color: #458; font-weight: 600;">double</span> <span class="no" style="color: #008080;">MAX_IBD_GAP_CM</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">4.0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</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">@@ -163,9 +164,8 @@ public final class Ibs2 {</td>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">wP1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">w</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">wP1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">wStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">wStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">wP1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nMarkers</span><span class="o" style="font-weight: 600;">();</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</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;">refGT</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</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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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">SampClust</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">equivLists</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> <span class="n" style="color: #333;">equivLists</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">SampClust</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">nSamples</span></span><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;">equivLists</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">initCluster</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">targGT</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">refGT</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">start</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">end</span></span><span class="o" style="font-weight: 600;">));</span></span>
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="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;">m</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">;</span></span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java"> <span class="n" style="color: #333;">equivLists</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">equivLists</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stream</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">@@ -175,10 +175,29 @@ public final class Ibs2 {</td>
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175
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">results</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">equivLists</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">());</span></span>
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176
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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177
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="java"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">SampClust</span> <span class="nf" style="color: #900; font-weight: 600;">initCluster</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</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;">start</span><span class="o" style="font-weight: 600;">,</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nTargSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">();</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</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;">refGT</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</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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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMiss</span> <span class="o" style="font-weight: 600;">=</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="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ceil</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">MAX_MISS_PROP</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">));</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java"> <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;">missCnt</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;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nSamples</span><span class="o" style="font-weight: 600;">];</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java"> <span class="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;">m</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" 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;">s</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;">s</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nTargSamples</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" 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;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">s</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;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">)==-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">missCnt</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">];</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></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>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> <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;">initCluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">IntStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">range</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;">nSamples</span><span class="o" style="font-weight: 600;">)</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">nTargSamples</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">missCnt</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">]<=</span><span class="n" style="color: #333;">maxMiss</span><span class="o" style="font-weight: 600;">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">();</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" 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;">SampClust</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">initCluster</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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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="java"></span>
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178
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">Stream</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">SampClust</span><span class="o" style="font-weight: 600;">></span> <span class="nf" style="color: #900; font-weight: 600;">partition</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span></span>
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179
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">SampClust</span> <span class="n" style="color: #333;">parent</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;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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180
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// this method assumes int[] parent.samples is sorted in increasing order</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> <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;"><span class="idiff left">a</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">];</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// alleles</span></span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="java"> <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;"><span class="idiff left">gt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">];</span></span></span>
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182
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nAlleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">nAlleles</span><span class="o" style="font-weight: 600;">();</span></span>
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183
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nTargSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">();</span></span>
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184
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">gtToList</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nAlleles</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nAlleles</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="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -186,8 +205,8 @@ public final class Ibs2 {</td>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">gtIndices</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">16</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="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">missingTargSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">32</span><span class="o" style="font-weight: 600;">);</span></span>
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188
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<pre style="margin: 0;"> <span id="LC207" 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;">s</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samples</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="LC189" class="line" lang="java"> <span class="n" style="color: #333;">setAlleles</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left right">a</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC190" 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;"><span class="idiff left">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]<</span></span><span class="mi" style="color: #099;"><span class="idiff">0</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">a</span></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 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="n" style="color: #333;">setAlleles</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left right">gt</span></span><span class="o" style="font-weight: 600;">);</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">gt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]<</span></span><span class="mi" style="color: #099;"><span class="idiff">0</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">gt</span></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 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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nTargSamples</span><span class="o" style="font-weight: 600;">;</span></span>
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192
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="java"> <span class="n" style="color: #333;">missingTargSamples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC212" 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;">k</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;">n</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gtIndices</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</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">@@ -195,13 +214,13 @@ public final class Ibs2 {</td>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="java"> <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="LC198" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gtIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]<=</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]*</span></span><span class="n" style="color: #333;"><span class="idiff">nAlleles</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">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]*</span></span><span class="n" style="color: #333;"><span class="idiff">nAlleles</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">a</span></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="LC217" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gtIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">gt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]<=</span></span><span class="n" style="color: #333;"><span class="idiff">gt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]*</span></span><span class="n" style="color: #333;"><span class="idiff">nAlleles</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">gt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]*</span></span><span class="n" style="color: #333;"><span class="idiff">nAlleles</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">gt</span></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="LC218" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gtToList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gtIndex</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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200
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="java"> <span class="n" style="color: #333;">gtToList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">);</span></span>
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201
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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202
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nTargSamples</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">missingTargSamples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">// assumes int[] parent.samples is increasing</span></span>
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203
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="java"> <span class="n" style="color: #333;">gtIndices</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"> <span class="n" style="color: #333;">areHom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">areHomozygous</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]==</span></span><span class="n" style="color: #333;"><span class="idiff right">a</span></span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="java"> <span class="n" style="color: #333;">areHom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">areHomozygous</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">gt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]==</span></span><span class="n" style="color: #333;"><span class="idiff right">gt</span></span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="java"> <span class="n" style="color: #333;">gtToList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</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="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;">k</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;">n</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">missingTargSamples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</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="c1" style="color: #998; font-style: italic;">// if s>=nTargSamples, put s in list w/ missTargSamples</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">@@ -212,8 +231,8 @@ public final class Ibs2 {</td>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gtIndices</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stream</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">gt</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">gtToList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">gt</span></span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()></span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mapToObj</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">gt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">SampClust</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gtToList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">gt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">toArray</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">areHom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">gt</span></span><span class="o" style="font-weight: 600;">]));</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">i</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">gtToList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()></span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mapToObj</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">SampClust</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gtToList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">toArray</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">areHom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span></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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setAlleles</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;">m</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;">s</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1#55b6fb2cf31c47611bc2ebee66d816160c3223ae"><strong>phase/ImputeBaum.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">@@ -197,7 +197,7 @@ public class ImputeBaum {</td>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hap</span><span class="o" style="font-weight: 600;">);</span></span>
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198
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hap</span> <span class="o" style="font-weight: 600;">^</span> <span class="mb">0b1</span><span class="o" style="font-weight: 600;">);</span></span>
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199
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">b1</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;">b2</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC200" 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;">b1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">b2</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="LC200" 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;">b1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">b2</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="n" style="color: #333;"><span class="idiff right">nTargHaps</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="LC201" class="line" lang="java"> <span class="n" style="color: #333;">alProbs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">prob</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1#d0875a14cecab64969d49fa0ec30b89961d311ed"><strong>phase/PhaseLS.java</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -67,7 +67,9 @@ public class PhaseLS {</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">updateRecombFactor</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ExecutorService</span> <span class="n" style="color: #333;">es</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="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">PhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</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="LC69" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">par</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nthreads</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxSumY</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mf" style="color: #099;">5000.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nThreads</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">200.0</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxSumY</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">5000.0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxThreadSumY</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">maxSumY</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nThreads</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">200.0</span><span class="o" style="font-weight: 600;">);</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxUpdates</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20000</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nThreads</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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71
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Regress</span> <span class="n" style="color: #333;">regress</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Regress</span><span class="o" style="font-weight: 600;">();</span></span>
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72
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">targGT</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">();</span></span>
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73
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">CountDownLatch</span> <span class="n" style="color: #333;">latch</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">CountDownLatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nThreads</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="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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,8 +77,9 @@ public class PhaseLS {</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">seed</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="java"> <span class="n" style="color: #333;">es</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">submit</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="LC79" 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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<pre style="margin: 0;">+<span id="LC80" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nUpdates</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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78
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">RecombRegress</span> <span class="n" style="color: #333;">rr</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">RecombRegress</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">regress</span><span class="o" style="font-weight: 600;">);</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sumY</span><span class="o" style="font-weight: 600;">()<</span><span class="n" style="color: #333;">max<span class="idiff left right">SumY</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">// thread-confined for reproducability</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC82" 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;">rr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sumY</span><span class="o" style="font-weight: 600;">()<</span><span class="n" style="color: #333;">max<span class="idiff left">ThreadSumY</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff">nUpdates</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">maxUpdates</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">// thread-confined for reproducability</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"> <span class="n" style="color: #333;">rr</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">update</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nSamples</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="java"> <span class="n" style="color: #333;">latch</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countDown</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="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="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,12 +91,12 @@ public class PhaseLS {</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MultiThreadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">await</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">latch</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">recombFactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">regress</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">beta</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recombFactor</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 class="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFinite</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recombFactor</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="LC94" 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;">regress</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sumY</span><span class="o" style="font-weight: 600;">()>=</span><span class="n" style="color: #333;">maxSumY</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">recombFactor</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.0</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFinite</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recombFactor</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="LC96" class="line" lang="java"> <span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setRecombFactor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recombFactor</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java"> <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="LC95" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"WARNING: no recombFactor update: "</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">recombFactor</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"WARNING: no recombFactor update"</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="java"></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1#1ac54fb4d23beda1b68dc539cae4477660958812"><strong>phase/RecombRegress.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">@@ -46,11 +46,11 @@ public class RecombRegress {</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC47" 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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hap1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"> <span class="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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">hap2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"> <span class="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;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="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;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="java"> <span class="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;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fwdM1</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="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;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">bwd</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="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;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">fwdM1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java"> <span class="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;">float</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">savedBwd</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"> <span class="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;"><span class="idiff left right">float</span></span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">pMismatch</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="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;"><span class="idiff left right">double</span></span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">pMismatch</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">HmmUpdater</span> <span class="n" style="color: #333;">hmmUpdater</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Regress</span> <span class="n" style="color: #333;">regress</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,13 +84,13 @@ public class RecombRegress {</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC85" 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: #008080;">hap1</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;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">];</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hap2</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;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">];</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">savedBwd</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;">float</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">maxStates</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fwd</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;">float</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">maxStates</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bwd</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;">float</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">maxStates</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fwdM1</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;">float</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">maxStates</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">pErr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pMismatch</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;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pErr</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pErr</span><span class="o" style="font-weight: 600;">};</span></span>
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<pre style="margin: 0;">-<span id="LC93" 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: #008080;">hmmUpdater</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HmmUpdater</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pErr</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">savedBwd</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;">float</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">maxStates</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">+<span id="LC89" 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: #008080;">fwd</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;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">maxStates</span><span class="o" style="font-weight: 600;">];</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" 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: #008080;">fwdM1</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;">double</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">maxStates</span><span class="o" style="font-weight: 600;">];</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pErr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">err</span><span class="o" style="font-weight: 600;">();</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" 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: #008080;">pMismatch</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;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pErr</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pErr</span><span class="o" style="font-weight: 600;">};</span></span>
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<pre style="margin: 0;">+<span id="LC93" 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: #008080;">hmmUpdater</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HmmUpdater</span><span class="o" style="font-weight: 600;">((</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">pErr</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC94" 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: #008080;">regress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">regress</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -126,31 +126,36 @@ public class RecombRegress {</td>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">hmmUpdater</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bwdUpdate</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bwd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pRecomb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mP1</span><span class="o" style="font-weight: 600;">),</span> <span class="n" style="color: #333;">alMatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">mP1</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">arraycopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bwd</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;">savedBwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">],</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">float</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hFactor</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">float</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="n" style="color: #333;"><span class="idiff">nStates</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nStates</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">1.0</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="LC129" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">hFactor</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">nStates</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nStates</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">1.0</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fill</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fwd</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;">nStates</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">1.0f</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">float</span></span> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">double</span></span> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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132
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<pre style="margin: 0;"> <span id="LC132" 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;">hmmUpdater</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fwdUpdate</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fwd</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 class="n" style="color: #333;">pRecomb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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="n" style="color: #333;">alMatch</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;">nStates</span><span class="o" style="font-weight: 600;">);</span></span>
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133
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<pre style="margin: 0;"> <span id="LC133" 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;">m</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;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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134
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<pre style="margin: 0;"> <span id="LC134" 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;">fwdUpdate</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">alMatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hFactor</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">fwdUpdate</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;">m</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;">alMatch</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">lastSum</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">hFactor</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="LC139" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">pSwitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pRecomb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pSwitch</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;">pSwitch</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">))/</span><span class="n" style="color: #333;">lastSum</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">partNumer</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">fwdUpdate</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;">m</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;">alMatch</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">lastSum</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">hFactor</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="LC139" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pSwitch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pRecomb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pSwitch</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pSwitch</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">lastSum</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">partScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pSwitch</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;">pSwitch</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">))/</span><span class="n" style="color: #333;">lastSum</span><span class="o" style="font-weight: 600;">;</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">numer</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="java"></span>
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144
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">storedBwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">savedBwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">];</span></span>
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145
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">arraycopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fwd</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;">fwdM1</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;">nStates</span><span class="o" style="font-weight: 600;">);</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">float</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sum</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">hmmUpdater</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">fwdUpdate</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fwd</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">lastSum</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">pRecomb</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">get</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">m</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">alMatch</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">nStates</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>;</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sum</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">0.0f</span></span><span class="o" style="font-weight: 600;">;</span></span>
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147
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150
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<pre style="margin: 0;"> <span id="LC150" 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;">k</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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java"> <span class="n" style="color: #333;">partNumer</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">pMismatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">alMatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]]*</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fwdM1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">storedBwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">];</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"> <span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pMismatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">alMatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]]*(</span><span class="n" style="color: #333;">scale</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fwdM1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">shift</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">partFwd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pMismatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">alMatch</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]]*(</span><span class="n" style="color: #333;">partScale</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fwdM1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]);</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="java"> <span class="n" style="color: #333;">numer</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]<</span><span class="n" style="color: #333;">partFwd</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 class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">partFwd</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">storedBwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">];</span></span>
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149
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="java"> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">]*</span><span class="n" style="color: #333;">storedBwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</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="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fwd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">];</span></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">partNumer</span><span class="o" style="font-weight: 600;">;</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">xVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genDist</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">);</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">yVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hFactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">denom</span><span class="o" style="font-weight: 600;">);</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">xVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genDist</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">);</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">yVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hFactor</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">numer</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">denom</span><span class="o" style="font-weight: 600;">);</span></span>
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154
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">regress</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xVal</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">yVal</span><span class="o" style="font-weight: 600;">);</span></span>
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155
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="java"> <span class="n" style="color: #333;">sumY</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">yVal</span><span class="o" style="font-weight: 600;">;</span></span>
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156
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sum</span><span class="o" style="font-weight: 600;">;</span></span>
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<li id="6ba560a119d50b4bdbe6c09549cb4a9204ac0f16">
<a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1#6ba560a119d50b4bdbe6c09549cb4a9204ac0f16"><strong>vcf/PlinkGenMap.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">@@ -349,7 +349,7 @@ public final class PlinkGenMap implements GeneticMap {</td>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="java"> <span class="nd">@Override</span></span>
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350
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350
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<pre style="margin: 0;"> <span id="LC350" 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;">basePos</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;">chrom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">geneticPosition</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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351
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="java"> <span class="n" style="color: #333;">checkChromIndex</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">);</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">minEndBasepairDist</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">5_000_00</span>0</span><span class="o" style="font-weight: 600;">;</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">minEndCmDist</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">5.</span>0</span><span class="o" style="font-weight: 600;">;</span></span>
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353
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353
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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;">mapSizeM1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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354
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mapSizeM1</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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355
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -361,42 +361,36 @@ public final class PlinkGenMap implements GeneticMap {</td>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">aIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insPt</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">mapSizeM1</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="LC364" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">basePos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</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">basePos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">mapSizeM1</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="n" style="color: #333;"><span class="idiff right">minEndBasepair</span>Dist</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="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">genPos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</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">genPos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">mapSizeM1</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="n" style="color: #333;"><span class="idiff right">minEndCm</span>Dist</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mapSizeM1</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="n" style="color: #333;">aIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</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="LC370" class="line" lang="java"> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC371" 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;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">]==</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="java"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">basePos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</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">basePos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">minEndBasepair</span>Dist</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">genPos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</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">genPos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="o" style="font-weight: 600;"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">minEndCm</span>Dist</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC374" 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;">insPt</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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378
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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379
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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380
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">insPt</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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381
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="java"> <span class="n" style="color: #333;">aIndex</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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382
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="java"> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">);</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">]==</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mapSizeM1</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="LC384" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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387
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">geneticPosition</span><span class="o" style="font-weight: 600;">;</span></span>
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388
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">];</span></span>
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">];</span></span>
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390
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">];</span></span>
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391
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">interp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">)/(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fb</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">interp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fa</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="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">)/(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fb</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">);</span></span>
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393
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<pre style="margin: 0;"> <span id="LC387" 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;">interp</span><span class="o" style="font-weight: 600;">>=</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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394
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Base position exceeds Integer.MAX_VALUE"</span></span>
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395
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">blbutil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span></span>
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396
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Are all genetic distances in cM units (in command line and in genetic map)?"</span><span class="o" style="font-weight: 600;">;</span></span>
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397
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<pre style="margin: 0;"> <span id="LC391" 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;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">);</span></span>
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398
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">fa</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="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="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">interp</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">interp</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="java"></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/commit/19dc404538b9e89018d2e394c77e29bbc8eb43b1#ec6a94af868b7dfb86724b44ca474651fa26375a"><strong>vcf/RefIt.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">@@ -55,18 +55,18 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The default number of {@code GTRec} objects that are</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * stored in a buffer.</span></span>
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<pre style="margin: 0;"> <span id="LC57" 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="LC58" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">DEFAULT_BUFFER_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="java"> <span class="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="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">DEFAULT_BUFFER_SIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="java"> <span class="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="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="no" style="color: #008080;">SENTINAL</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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="LC60" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC61" 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;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">stopFileReading</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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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="java"></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">VcfHeader</span> <span class="n" style="color: #333;">vcfHeader</span><span class="o" style="font-weight: 600;">;</span></span>
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61
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">FileIt</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">;</span></span>
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62
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Function</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mapper</span><span class="o" style="font-weight: 600;">;</span></span>
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63
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Filter</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">Marker</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">markerFilter</span><span class="o" style="font-weight: 600;">;</span></span>
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64
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastChrom</span><span class="o" style="font-weight: 600;">;</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" 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;">eof</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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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"></span>
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68
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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;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]></span> <span class="n" style="color: #333;">stringBuffer</span><span class="o" style="font-weight: 600;">;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;"><span class="idiff left right">mid</span>Buffer</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;"><span class="idiff left right">lowFreq</span>Buffer</span><span class="o" style="font-weight: 600;">;</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Deque</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">recBuffer</span><span class="o" style="font-weight: 600;">;</span></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">SeqCoder3</span> <span class="n" style="color: #333;">seqCoder</span><span class="o" style="font-weight: 600;">;</span></span>
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72
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<pre style="margin: 0;"> <span id="LC72" 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;">maxSeqCodedAlleles</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="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -74,6 +74,8 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">ExecutorService</span> <span class="n" style="color: #333;">es</span><span class="o" style="font-weight: 600;">;</span></span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastChrom</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>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC79" 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="LC80" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Create and returns a new {@code RefIt} instance from the specified</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * iterator.</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">@@ -146,9 +148,8 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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<pre style="margin: 0;"> <span id="LC148" 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: #008080;">maxSeqCodedAlleles</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">seqCoder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">maxNSeq</span><span class="o" style="font-weight: 600;">(),</span> <span class="nc" style="color: #458; font-weight: 600;">SeqCoder3</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_NALLELES</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 class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">maxSeqCodingMajorCnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxSeqCodingMajorCnt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">vcfHeader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samples</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC149" 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: #008080;">lastChrom</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>
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<pre style="margin: 0;"> <span id="LC151" 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: #008080;">stringBuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><>(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" 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: #008080;"><span class="idiff left right">mid</span>Buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<pre style="margin: 0;">+<span id="LC152" 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: #008080;"><span class="idiff left right">lowFreq</span>Buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>();</span></span>
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<pre style="margin: 0;"> <span id="LC153" 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: #008080;">recBuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayDeque</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">bufferSize</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>
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<pre style="margin: 0;"> <span id="LC155" 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: #008080;">es</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Executors</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">newSingleThreadExecutor</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">@@ -165,35 +166,45 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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165
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]></span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">firstRec</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">FileIt</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">it</span><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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bufferSize</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="LC168" class="line" lang="java"> <span class="n" style="color: #333;">es</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">submit</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="LC168" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">bufferSize</span><span class="o" style="font-weight: 600;">);</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="java"> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">firstRec</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC170" 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;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">bufferSize</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MultiThreadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">putInBlockingQ</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sa</span><span class="o" style="font-weight: 600;">);</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="java"> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">bufferSize</span><span class="o" style="font-weight: 600;">);</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="java"> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">firstRec</span><span class="o" style="font-weight: 600;">);</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" 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;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">bufferSize</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" 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;">stopFileReading</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java"> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" 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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177
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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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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MultiThreadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">putInBlockingQ</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sa</span><span class="o" style="font-weight: 600;">);</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java"> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="java"> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">());</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="java"> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java"> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="java"> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">SENTINAL</span><span class="o" style="font-weight: 600;">);</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="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="nc" style="color: #458; font-weight: 600;">InterruptedException</span> <span class="n" style="color: #333;">ex</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exit</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ERROR: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">ex</span><span class="o" style="font-weight: 600;">);</span></span>
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175
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="java"> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">());</span></span>
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177
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="java"> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</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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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> <span class="n" style="color: #333;">recs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="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="nc" style="color: #458; font-weight: 600;">InterruptedException</span> <span class="n" style="color: #333;">ex</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exit</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ERROR: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">file</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">ex</span><span class="o" style="font-weight: 600;">);</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="java"> <span class="k" style="font-weight: 600;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Throwable</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exit</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>
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185
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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186
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="java"> <span class="o" style="font-weight: 600;">});</span></span>
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187
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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188
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java"></span>
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189
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200
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<pre style="margin: 0;"> <span id="LC200" 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;">fillEmissionBuffer</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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190
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isEmpty</span><span class="o" style="font-weight: 600;">();</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">finished</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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192
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<pre style="margin: 0;">-<span id="LC192" 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;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isEmpty</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">finished</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="o" style="font-weight: 600;">{</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isEmpty</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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193
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sa</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">MultiThreadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">takeFromBlockingQ</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stringBuffer</span><span class="o" style="font-weight: 600;">);</span></span>
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194
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<td class="diff-line-num new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
204
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<pre style="margin: 0;"> <span id="LC204" 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;">sa</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="java"> <span class="n" style="color: #333;">finished</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 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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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="java"> <span class="n" style="color: #333;">stringBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sa</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// put sentinal back in qeueue</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="java"> <span class="n" style="color: #333;">flushToRecBuffer</span><span class="o" style="font-weight: 600;">();</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;</span></span>
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197
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208
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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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198
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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199
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">recs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseLines</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sa</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">@@ -203,29 +214,25 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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<pre style="margin: 0;"> <span id="LC214" 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;">lastChrom</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 class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="java"> <span class="n" style="color: #333;">lastChrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="java"> <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;">chrom</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">lastChrom</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;"><span class="idiff left right">mid</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()==</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</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;">flush<span class="idiff left right">MidBuffer</span>ToRecBuffer</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC217" 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;">chrom</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">lastChrom</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;"><span class="idiff left right">lowFreq</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()==</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</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="LC218" class="line" lang="java"> <span class="n" style="color: #333;">flushToRecBuffer</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="java"> <span class="n" style="color: #333;">lastChrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC221" 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;">applySeqCoding</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="kc" style="font-weight: 600;">false</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="LC211" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">mid</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</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="LC222" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">lowFreq</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</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="LC223" class="line" lang="java"> <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 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="LC225" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqCoder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</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="LC226" 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;">success</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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java"> <span class="n" style="color: #333;">flush<span class="idiff left right">MidBuffer</span>ToRecBuffer</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="n" style="color: #333;">flushToRecBuffer</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="n" style="color: #333;">success</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqCoder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</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="LC229" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">success</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">mid</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</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="LC231" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">lowFreq</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</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="LC232" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="java"> <span 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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">finished</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="n" style="color: #333;">flushMidBufferToRecBuffer</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="n" style="color: #333;">eof</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="LC228" class="line" lang="java"> <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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">parseLines</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">lines</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">@@ -236,29 +243,30 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span><span class="o" style="font-weight: 600;">[]::</span><span class="k" style="font-weight: 600;">new</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">flush<span class="idiff left right">MidBuffer</span>ToRecBuffer</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="LC246" 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;">flushToRecBuffer</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="LC247" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">RefGTRec</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;">seqCoder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getCompressedList</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC242" 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;">j</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;">n</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left right">mid</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">GTRec</span> <span class="n" style="color: #333;">ve</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">mid</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" 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;">j</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;">n</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left right">lowFreq</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">GTRec</span> <span class="n" style="color: #333;">ve</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">lowFreq</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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244
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251
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<pre style="margin: 0;"> <span id="LC251" 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;">ve</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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<pre style="margin: 0;">-<span id="LC245" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">mid</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">++));</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">lowFreq</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">++));</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="java"> <span class="n" style="color: #333;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left right">mid</span>Buffer</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left right">mid</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="java"> <span class="n" style="color: #333;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addAll</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left right">lowFreq</span>Buffer</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="n" style="color: #333;"><span class="idiff left right">lowFreq</span>Buffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;"> <span id="LC260" 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;">close</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="LC254" class="line" lang="java"> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="java"> <span class="n" style="color: #333;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</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="n" style="color: #333;">midBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// empty string buffer in order to stop ExecutorService</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="java"> <span class="n" style="color: #333;">stopFileReading</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="LC262" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// empty string buffer</span></span>
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258
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sa</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">MultiThreadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">takeFromBlockingQ</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stringBuffer</span><span class="o" style="font-weight: 600;">);</span></span>
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259
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264
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<pre style="margin: 0;"> <span id="LC264" 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;">sa</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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260
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="java"> <span class="n" style="color: #333;">sa</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">MultiThreadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">takeFromBlockingQ</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stringBuffer</span><span class="o" style="font-weight: 600;">);</span></span>
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261
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="java"> <span class="n" style="color: #333;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="java"> <span class="n" style="color: #333;">lowFreqBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="java"> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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262
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MultiThreadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">shutdownExecService</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">es</span><span class="o" style="font-weight: 600;">);</span></span>
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263
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="java"> <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>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -283,7 +291,7 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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283
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<pre style="margin: 0;"> <span id="LC291" 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;">NoSuchElementException</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">removeFirst</span><span class="o" style="font-weight: 600;">();</span></span>
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286
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<pre style="margin: 0;">-<span id="LC286" 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;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isEmpty</span><span class="o" style="font-weight: 600;">()</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">eof</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="kc" style="font-weight: 600;"><span class="idiff right">false</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recBuffer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isEmpty</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="LC295" class="line" lang="java"> <span class="n" style="color: #333;">fillEmissionBuffer</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">;</span></span>
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