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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/17c4ecf0446518fbdf7063b525bdd875d10535b1">17c4ecf0</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-10-14T19:28:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.1-190921+dfsg</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#315086b42467cd64d67b45236c874d197c068244">
imp/ImpStates.java
</a>
</li>
<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
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</li>
<li class="file-stats">
<a href="#55b6fb2cf31c47611bc2ebee66d816160c3223ae">
phase/ImputeBaum.java
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</li>
<li class="file-stats">
<a href="#3b2984bf7adf228997d3b8dee46dcd4ce716b5c9">
phase/PhaseStates.java
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<li class="file-stats">
<a href="#3e06eef3ae51629718f58b9d354c9179c61b3f04">
vcf/AllData.java
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<li class="file-stats">
<a href="#78fa00826ae554b25eb82635d04cb923a65a3707">
vcf/BitSetGTRec.java
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</li>
</ul>
<h4>Changes:</h4>
<li id="315086b42467cd64d67b45236c874d197c068244">
<a href="https://salsa.debian.org/med-team/beagle/commit/17c4ecf0446518fbdf7063b525bdd875d10535b1#315086b42467cd64d67b45236c874d197c068244"><strong>imp/ImpStates.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">@@ -40,13 +40,13 @@ public final class ImpStates {</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">NIL</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">103</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">ImpIbs</span> <span class="n" style="color: #333;">ibsHaps</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="java"> <span class="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;">ImpData</span> <span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="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;">maxStates</span><span class="o" style="font-weight: 600;">;</span></span>
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43
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<pre style="margin: 0;"> <span id="LC43" 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;">nClusters</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="java"> <span class="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;">maxStates</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;">final</span> <span class="nc" style="color: #458; font-weight: 600;">IntIntMap</span> <span class="n" style="color: #333;">hapToEnd</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;">PriorityQueue</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">CompHapSegment</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>
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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;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">comp<span class="idiff left right">HapToHapList</span></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="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">comp<span class="idiff left right">HapToEndList</span></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;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">comp<span class="idiff left right">ositeHapToHap</span></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="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">comp<span class="idiff left right">ositeHapToEnd</span></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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">compHapToListIndex</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;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">compHapToHap</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">@@ -64,10 +64,10 @@ public final class ImpStates {</td>
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<pre style="margin: 0;"> <span id="LC64" 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;">maxStates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">impData</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;">imp_states</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hapToEnd</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;">IntIntMap</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="LC66" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">q</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;">PriorityQueue</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="LC67" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">comp<span class="idiff left right">HapToHapList</span></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;">maxStates</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">comp<span class="idiff left right">ositeHapToHap</span></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;">maxStates</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="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;">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;">IntList</span><span class="o" style="font-weight: 600;">())</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">IntList</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="LC70" 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;">comp<span class="idiff left right">HapToEndList</span></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;">maxStates</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">comp<span class="idiff left right">ositeHapToEnd</span></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;">maxStates</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="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;">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;">IntList</span><span class="o" style="font-weight: 600;">())</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"> <span class="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;">IntList</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="LC73" 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;">compHapToListIndex</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;">maxStates</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">@@ -76,11 +76,11 @@ public final class ImpStates {</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"></span>
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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="cm" style="color: #998; font-style: italic;"> * Returns the <span class="idiff left right">input data for genotype imputation</span>.</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;"> * @return the <span class="idiff left right">input data for genotype imputation</span></span></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;"> * Returns the <span class="idiff left right">maximum number of HMM states at a marker</span>.</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;"> * @return the <span class="idiff left right">maximum number of HMM states at a marker</span></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;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">ImpData</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff right">impData</span></span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">impData</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff right">maxStates</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="LC83" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">maxStates</span></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>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="diff-line-num unfold js-unfold 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">@@ -91,7 +91,7 @@ public final class ImpStates {</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * at the {@code m}-th marker in {@code alMatch[m][j]}. The number of</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * HMM states states at each marker is returned.</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;"> * @param targHap the haplotype index</span></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;"> * @param hap<span class="idiff left right">Indice</span>s the two-dimensional array in which</span></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;"> * @param haps the two-dimensional array in which</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;"> * reference haplotype indices for each HMM state will be stored</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;"> * @param alMatch the two-dimensional array in which allele match status</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;"> * between the target haplotype and HMM state will be stored</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">@@ -104,7 +104,7 @@ public final class ImpStates {</td>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * HMM states</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws NullPointerException if any array is {@code null}</span></span>
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<pre style="margin: 0;"> <span id="LC106" 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="LC107" 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;">ibsStates</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;">targHap</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;">hap<span class="idiff left right">Indice</span>s</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">alMatch</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="LC107" 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;">ibsStates</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;">targHap</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;">haps</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">alMatch</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="LC108" class="line" lang="java"> <span class="n" style="color: #333;">initializeFields</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java"> <span class="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;">ibsHaps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">codedSteps</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nSteps</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="LC110" 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;">ibs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ibsHaps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ibsHaps</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targHap</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,93 +115,93 @@ public final class ImpStates {</td>
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<pre style="margin: 0;"> <span id="LC115" 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;">q</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="LC116" class="line" lang="java"> <span class="n" style="color: #333;">fillQWithRandomHaps</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targHap</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numStates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copyData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targHap</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hap<span class="idiff left right">Indice</span>s</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>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numStates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copyData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targHap</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">haps</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>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numStates</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC122" 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;">initializeFields</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="LC123" class="line" lang="java"> <span class="n" style="color: #333;">hapToEnd</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="LC124" 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;">q</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="LC125" class="line" lang="java"> <span class="n" style="color: #333;">comp<span class="idiff left right">HapToHapList</span></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="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="LC126" class="line" lang="java"> <span class="n" style="color: #333;">comp<span class="idiff left right">HapToEndList</span></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="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="LC125" class="line" lang="java"> <span class="n" style="color: #333;">comp<span class="idiff left right">ositeHapToHap</span></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="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="LC126" class="line" lang="java"> <span class="n" style="color: #333;">comp<span class="idiff left right">ositeHapToEnd</span></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="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="LC127" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java"> <span class="n" style="color: #333;">q</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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129
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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130
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java"></span>
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131
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131
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<pre style="margin: 0;"> <span id="LC131" 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;">updateFields</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="n" style="color: #333;">step</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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132
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132
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<pre style="margin: 0;"> <span id="LC132" 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;">hapToEnd</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;">hap</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">NIL</span><span class="o" style="font-weight: 600;">)==</span><span class="no" style="color: #008080;">NIL</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;">// hap not currently in q</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"> <span class="n" style="color: #333;">updateHeadOfQ</span><span class="o" style="font-weight: 600;">();</span></span>
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133
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134
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<pre style="margin: 0;"> <span id="LC134" 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;">q</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;">maxStates</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="nc" style="color: #458; font-weight: 600;">CompHapSegment</span> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">updateHeadAndPoll</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="n" style="color: #333;">hapToEnd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hap</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="nc" style="color: #458; font-weight: 600;">CompHapSegment</span> <span class="n" style="color: #333;">head</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="na" style="color: #008080;">poll</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">modEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ibsHaps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">codedSteps</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">stepStart</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">step</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">step</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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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">compHapToHapList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">head</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">compHapIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()].</span></span><span class="na" style="color: #008080;"><span class="idiff">add</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></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="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// hap of new segment</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> <span class="n" style="color: #333;">comp<span class="idiff left">HapToEndList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">head</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">compHapIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()].</span></span><span class="na" style="color: #008080;"><span class="idiff">add</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">modEnd</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">// end of old</span> segment</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="java"> <span class="n" style="color: #333;"><span class="idiff left">hapToEnd</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">remove</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">head</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">hap</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">());</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> <span class="n" style="color: #333;">comp<span class="idiff left">ositeHapToHap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">head</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">compHapIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()].</span></span><span class="na" style="color: #008080;"><span class="idiff">add</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></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="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// hap of new</span> segment</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> <span class="n" style="color: #333;">compositeHapToEnd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compHapIndex</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;">modEnd</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// end of old segment</span></span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="java"> <span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateHap</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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141
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="java"> <span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateStep</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">step</span><span class="o" style="font-weight: 600;">);</span></span>
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142
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142
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<pre style="margin: 0;"> <span id="LC142" 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;">offer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">);</span></span>
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143
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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144
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144
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<pre style="margin: 0;"> <span id="LC144" 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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145
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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;">int</span> <span class="n" style="color: #333;">compHapIndex</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="na" style="color: #008080;">size</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="n" style="color: #333;">comp<span class="idiff left right">HapToHapList</span></span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">compHapIndex</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;">hap</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// hap of new segment</span></span>
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<td class="diff-line-num new old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java"> <span class="n" style="color: #333;">comp<span class="idiff left right">ositeHapToHap</span></span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">compHapIndex</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;">hap</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// hap of new segment</span></span>
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147
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147
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<pre style="margin: 0;"> <span id="LC147" 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;">offer</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;">CompHapSegment</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;">step</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">compHapIndex</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="o" style="font-weight: 600;">}</span></span>
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149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="java"> <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="n" style="color: #333;">hapToEnd</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;">hap</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">step</span><span class="o" style="font-weight: 600;">);</span></span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="java"> <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>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nc" style="color: #458; font-weight: 600;">CompHapSegment</span> <span class="nf" style="color: #900; font-weight: 600;">updateHeadAndPoll</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">CompHapSegment</span> <span class="n" style="color: #333;">head</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="na" style="color: #008080;">poll</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="LC155" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">latestEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hapToEnd</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;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hap</span><span class="o" style="font-weight: 600;">(),</span> <span class="no" style="color: #008080;">NIL</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="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">step</span><span class="o" style="font-weight: 600;">()!=</span><span class="n" style="color: #333;">latestEnd</span><span class="o" style="font-weight: 600;">)</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="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateStep</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">latestEnd</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="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">offer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">head</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="na" style="color: #008080;">poll</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java"> <span class="n" style="color: #333;">latestEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hapToEnd</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;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hap</span><span class="o" style="font-weight: 600;">(),</span> <span class="no" style="color: #008080;">NIL</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">;</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java"></span>
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165
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<pre style="margin: 0;">-<span id="LC165" 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;">fillQWithRandomHaps</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="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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">q</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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167
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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;">nHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">impData</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>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nStates</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;">nHaps</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;">maxStates</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</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="mi" style="color: #099;">1</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;">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;">hap</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;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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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;">int</span> <span class="n" style="color: #333;">h</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;">nHaps</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;">while</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)==</span><span class="n" style="color: #333;">sample</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="n" style="color: #333;">h</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;">nHaps</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="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;">updateHeadOfQ</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">CompHapSegment</span> <span class="n" style="color: #333;">head</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="na" style="color: #008080;">peek</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="LC155" 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;">head</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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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">latestEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hapToEnd</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;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hap</span><span class="o" style="font-weight: 600;">(),</span> <span class="no" style="color: #008080;">NIL</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="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">step</span><span class="o" style="font-weight: 600;">()!=</span><span class="n" style="color: #333;">latestEnd</span><span class="o" style="font-weight: 600;">)</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="n" style="color: #333;">head</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="na" style="color: #008080;">poll</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateStep</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">latestEnd</span><span class="o" style="font-weight: 600;">);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" 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;">offer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">);</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="java"> <span class="n" style="color: #333;">head</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="na" style="color: #008080;">peek</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="java"> <span class="n" style="color: #333;">latestEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hapToEnd</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;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hap</span><span class="o" style="font-weight: 600;">(),</span> <span class="no" style="color: #008080;">NIL</span><span class="o" style="font-weight: 600;">);</span></span>
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175
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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176
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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC176" 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;">add</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;">CompHapSegment</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;">nClusters</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">));</span></span>
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177
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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178
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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179
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java"></span>
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180
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167
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">copyData</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;">targHap</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;">hapIndices</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">alMatch</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nCompHaps</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="na" style="color: #008080;">size</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nCompositeHaps</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="na" style="color: #008080;">size</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;">initializeCopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nCompositeHaps</span><span class="o" style="font-weight: 600;">);</span></span>
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182
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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;">shiftedTargHap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nRefHaps</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">targHap</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="n" style="color: #333;">initializeCopy</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nCompHaps</span><span class="o" style="font-weight: 600;">);</span></span>
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184
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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;">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;">0</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;">nClusters</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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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targAl<span class="idiff left right">lele</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">impData</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;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">shiftedTargHap</span><span class="o" style="font-weight: 600;">);</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="java"> <span class="k" style="font-weight: 600;">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;">nCompHaps</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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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;">int</span> <span class="n" style="color: #333;">targAl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">impData</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;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">shiftedTargHap</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" 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;">nComp<span class="idiff left right">osite</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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187
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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
174
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<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;">m</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">compHapToEnd</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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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">compHapToListIndex</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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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compHapToHapList</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compHapToEndList</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compositeHapToHap</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compositeHapToEnd</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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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<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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nRefHaps</span><span class="o" style="font-weight: 600;">();</span></span>
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191
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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
192
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<td class="diff-line-num new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="java"> <span class="n" style="color: #333;">hapIndices</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;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compHapToHap</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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<td class="diff-line-num old old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
193
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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"> <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;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">impData</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;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">compHapToHap</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;">targAl<span class="idiff left right">lele</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <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;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">impData</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;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">compHapToHap</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;">targAl</span><span class="o" style="font-weight: 600;">;</span></span>
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194
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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195
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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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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nCompHaps</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;">return</span> <span class="n" style="color: #333;">nComp<span class="idiff left right">osite</span>Haps</span><span class="o" style="font-weight: 600;">;</span></span>
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197
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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198
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="java"></span>
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199
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187
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<pre style="margin: 0;"> <span id="LC187" 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;">initializeCopy</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;">nSlots</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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188
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<pre style="margin: 0;"> <span id="LC188" 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;">nSlots</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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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java"> <span class="n" style="color: #333;">comp<span class="idiff left right">HapToEndList</span></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="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nClusters</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// add missing end of last segment</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;">comp<span class="idiff left right">ositeHapToEnd</span></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="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nClusters</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// add missing end of last segment</span></span>
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202
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="java"> <span class="n" style="color: #333;">compHapToListIndex</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 class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compHapToHapList</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="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>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compHapToEndList</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="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>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compositeHapToHap</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="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>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compositeHapToEnd</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="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>
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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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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="java"> <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>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" 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;">fillQWithRandomHaps</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="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">q</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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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">nRefHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nRefHaps</span><span class="o" style="font-weight: 600;">();</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" 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="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;">nRefHaps</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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200
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<pre style="margin: 0;">+<span id="LC200" 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;">hap</span><span class="o" style="font-weight: 600;">);</span></span>
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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;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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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;">h</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;">nRefHaps</span><span class="o" style="font-weight: 600;">);</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="java"> <span class="n" style="color: #333;">compositeHapToHap</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">add</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="c1" style="color: #998; font-style: italic;">// hap of new segment</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" 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;">add</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;">CompHapSegment</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;">nClusters</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">));</span></span>
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205
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="java"> <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="o" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/beagle/commit/17c4ecf0446518fbdf7063b525bdd875d10535b1#2ad0efaccf66628e1858a4c133e8914e33eb2221"><strong>main/Main.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">@@ -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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<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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67
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67
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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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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">4Aug19.3e8</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">4Aug19.3e8</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="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">1Sep19.ec3</span>.jar"</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;">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">1Sep19.ec3</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"></span>
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71
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71
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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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72
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72
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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="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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81
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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">4Aug19.3e8</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">1Sep19.ec3</span>.jar\" to "</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"list command line argument"</span><span class="o" style="font-weight: 600;">;</span></span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"></span>
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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/17c4ecf0446518fbdf7063b525bdd875d10535b1#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">@@ -23,6 +23,7 @@ import ints.IntArray;</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ints.IntList</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Random</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">vcf.GT</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">vcf.RefGT</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC28" 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="LC29" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * <p>Class {@code ImputeBaum} applies the forward and backward algorithms</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">@@ -48,7 +49,10 @@ public class ImputeBaum {</td>
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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="nc" style="color: #458; font-weight: 600;">FloatList</span> <span class="n" style="color: #333;">savedProbs</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;">FloatList</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">8</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;">hiFreqPhasedGT</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="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">allUnphasedGT</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="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">unphTargGT</span><span class="o" style="font-weight: 600;">;</span></span>
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53
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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="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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54
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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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nTargHaps</span><span class="o" style="font-weight: 600;">;</span></span>
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55
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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="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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52
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56
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<pre style="margin: 0;"> <span id="LC56" 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;">nHiFreqMarkers</span><span class="o" style="font-weight: 600;">;</span></span>
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57
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<pre style="margin: 0;"> <span id="LC57" 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;">HapImputer</span> <span class="n" style="color: #333;">imputableHaps</span><span class="o" style="font-weight: 600;">;</span></span>
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58
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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;">final</span> <span class="nc" style="color: #458; font-weight: 600;">IntArray</span> <span class="n" style="color: #333;">hiFreqIndices</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">@@ -74,11 +78,14 @@ public class ImputeBaum {</td>
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74
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78
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<pre style="margin: 0;"> <span id="LC78" 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;">probs</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">nHiFreqMarkers</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">fwdBwd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">maxStates</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>
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76
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<pre style="margin: 0;"> <span id="LC80" 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;">hiFreqPhasedGT</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;">estPhase</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">hapsGT</span><span class="o" style="font-weight: 600;">();</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allUnphasedGT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</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>
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81
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<pre style="margin: 0;">+<span id="LC81" 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;">unphTargGT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</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>
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82
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<pre style="margin: 0;">+<span id="LC82" 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;">refGT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">refGT</span><span class="o" style="font-weight: 600;">();</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nTargHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</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;">nHaps</span><span class="o" style="font-weight: 600;">();</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="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="n" style="color: #333;">fpd</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>
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78
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85
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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;">imputableHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hapImputer</span><span class="o" style="font-weight: 600;">;</span></span>
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79
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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;">hiFreqIndices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hiFreqIndices</span><span class="o" style="font-weight: 600;">();</span></span>
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80
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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;">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>
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<pre style="margin: 0;">-<span id="LC81" 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;">outPhase</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left right">allUnphased</span>GT</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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<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;">outPhase</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left right">unphTarg</span>GT</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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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"> <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>
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<pre style="margin: 0;"> <span id="LC91" 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">@@ -109,15 +116,15 @@ public class ImputeBaum {</td>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="java"> <span class="n" style="color: #333;">outPhase</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;">end</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hiFreqPhasedGT</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;">j</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"> <span class="n" style="color: #333;">start</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="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="LC118" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> <span class="n" style="color: #333;">imputeInterval</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sample</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;"><span class="idiff left right">allUnphased</span>GT</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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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"> <span class="n" style="color: #333;">imputeInterval</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sample</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;"><span class="idiff left right">unphTarg</span>GT</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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<pre style="margin: 0;"> <span id="LC120" class="line" lang="java"> <span class="n" style="color: #333;">imputableHaps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setHap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targHap</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;">outPhase</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="LC121" class="line" lang="java"> <span class="n" style="color: #333;">imputableHaps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setHap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targHap</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;">outPhase</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="LC122" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC124" 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;">imputeInterval</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;">sample</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 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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118
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<pre style="margin: 0;"> <span id="LC125" 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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<pre style="margin: 0;">-<span id="LC119" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">allUnphased</span>GT</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;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">allUnphased</span>GT</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;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">unphTarg</span>GT</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;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">unphTarg</span>GT</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;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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121
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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
128
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<pre style="margin: 0;"> <span id="LC128" 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;">a1</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;">a2</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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122
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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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;">boolean</span> <span class="n" style="color: #333;">noFlip</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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123
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130
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<pre style="margin: 0;"> <span id="LC130" 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;">a1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -138,7 +145,7 @@ public class ImputeBaum {</td>
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138
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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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139
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<td class="diff-line-num new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="java"></span>
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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
140
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<td class="diff-line-num new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
147
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<pre style="margin: 0;"> <span id="LC147" 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="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">unscaledAlProbs</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;">hapBit</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;">a1</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;">a2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
141
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<td class="diff-line-num new_line old" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC141" 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="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;"><span class="idiff left right">allUnphased</span>GT</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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<td class="diff-line-num new old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" 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="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;"><span class="idiff left right">unphTarg</span>GT</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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142
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<td class="diff-line-num new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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;">boolean</span> <span class="n" style="color: #333;">rare1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isLowFreq</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;">a1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
143
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">rare2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isLowFreq</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;">a2</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
144
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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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;">int</span> <span class="n" style="color: #333;">mkrA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">prevHiFreqMarker</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -148,8 +155,8 @@ public class ImputeBaum {</td>
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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
148
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155
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<pre style="margin: 0;"> <span id="LC155" 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;">probsB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">probs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">hapBit</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">mkrB</span><span class="o" style="font-weight: 600;">];</span></span>
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149
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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
156
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<pre style="margin: 0;"> <span id="LC156" 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;">nStates</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">hapBit</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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150
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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;">int</span> <span class="n" style="color: #333;">hap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">statesA</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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151
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<td class="diff-line-num new_line old" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC151" 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;">all<span class="idiff left">UnphasedGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">all</span>ele</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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152
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<td class="diff-line-num new_line old" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC152" 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;">all<span class="idiff left">UnphasedGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">all</span>ele</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 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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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">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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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" 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="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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153
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160
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<pre style="margin: 0;"> <span id="LC160" 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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154
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">wt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">prevWt</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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155
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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wt</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probsA</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 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;">wt</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">probsB</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -176,7 +183,7 @@ public class ImputeBaum {</td>
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176
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183
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<pre style="margin: 0;"> <span id="LC183" 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="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;">hapBit</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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177
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="java"> <span class="n" style="color: #333;">savedStates</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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178
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="java"> <span class="n" style="color: #333;">savedProbs</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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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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;">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="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;"><span class="idiff left right">allUnphased</span>GT</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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<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="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="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;"><span class="idiff left right">unphTarg</span>GT</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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180
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">unknownAlProb</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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181
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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;">mkrA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">prevHiFreqMarker</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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<td class="diff-line-num old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
182
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mkrB</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;">mkrA</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;">nHiFreqMarkers</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,8 +194,8 @@ public class ImputeBaum {</td>
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187
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">wt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">prevWt</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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188
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wt</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">probsA</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 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;">wt</span><span class="o" style="font-weight: 600;">)*</span><span class="n" style="color: #333;">probsB</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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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="java"> <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="n" style="color: #333;">statesA</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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<pre style="margin: 0;">-<span id="LC190" 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;">all<span class="idiff left">UnphasedGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">all</span>ele</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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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;">b2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all<span class="idiff left">UnphasedGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">all</span>ele</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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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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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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192
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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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193
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200
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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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194
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201
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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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -208,6 +215,18 @@ public class ImputeBaum {</td>
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208
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">imputedAllele</span><span class="o" style="font-weight: 600;">;</span></span>
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209
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216
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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="LC217" class="line" lang="java"></span>
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218
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<pre style="margin: 0;">+<span id="LC218" 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;">allele</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 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="o" style="font-weight: 600;">{</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" 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;">hap</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>
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220
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<pre style="margin: 0;">+<span id="LC220" 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;">IndexOutOfBoundsException</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="na" style="color: #008080;">valueOf</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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<pre style="margin: 0;">+<span id="LC221" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nTargHaps</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="LC223" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">unphTargGT</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;">hap</span><span class="o" style="font-weight: 600;">);</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" 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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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">refGT</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;">hap</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nTargHaps</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java"> <span class="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;">maxIndex</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;">fa</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxIndex</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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232
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<pre style="margin: 0;"> <span id="LC232" 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;">1</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;">fa</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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<a href="https://salsa.debian.org/med-team/beagle/commit/17c4ecf0446518fbdf7063b525bdd875d10535b1#3b2984bf7adf228997d3b8dee46dcd4ce716b5c9"><strong>phase/PhaseStates.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">@@ -47,8 +47,8 @@ public final class PhaseStates {</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">IntIntMap</span> <span class="n" style="color: #333;">hapToEnd</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="nc" style="color: #458; font-weight: 600;">PriorityQueue</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">CompHapSegment</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>
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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="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">compositeHapHap</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="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">compositeHapEnd</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="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>Hap</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="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>End</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>
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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;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">compHapToListIndex</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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">compHapToHap</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">@@ -75,10 +75,10 @@ public final class PhaseStates {</td>
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<pre style="margin: 0;"> <span id="LC75" 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;">minSteps</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="n" style="color: #333;">defaultMinSteps</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">scaleFactor</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hapToEnd</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;">IntIntMap</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="LC77" 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;">q</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;">PriorityQueue</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="LC78" 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;">compositeHapHap</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;">maxStates</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compositeHap<span class="idiff left right">To</span>Hap</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;">maxStates</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="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;">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;">IntList</span><span class="o" style="font-weight: 600;">())</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">IntList</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="LC81" 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;">compositeHapEnd</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;">maxStates</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compositeHap<span class="idiff left right">To</span>End</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;">maxStates</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mapToObj</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;">IntList</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 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;">IntList</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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84
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<pre style="margin: 0;"> <span id="LC84" 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;">compHapToListIndex</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;">maxStates</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="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -200,8 +200,8 @@ public final class PhaseStates {</td>
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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;">initializeFields</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;">hapToEnd</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="LC202" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">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;">q</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="LC203" class="line" lang="java"> <span class="n" style="color: #333;">compositeHapHap</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="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="LC204" class="line" lang="java"> <span class="n" style="color: #333;">compositeHapEnd</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="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="LC203" class="line" lang="java"> <span class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>Hap</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="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="LC204" class="line" lang="java"> <span class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>End</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="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="LC205" 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="n" style="color: #333;">q</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="LC207" 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">@@ -224,15 +224,15 @@ public final class PhaseStates {</td>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">CompHapSegment</span> <span class="n" style="color: #333;">head</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="na" style="color: #008080;">poll</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;">int</span> <span class="n" style="color: #333;">modEnd</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;">codedSteps</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">stepStart</span><span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">step</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">step</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="LC226" class="line" lang="java"> <span class="n" style="color: #333;">hapToEnd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hap</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;">compositeHapHap</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compHapIndex</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;">hap</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// hap of new segment</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="java"> <span class="n" style="color: #333;">compositeHapEnd</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compHapIndex</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;">modEnd</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// end of old segment</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="java"> <span class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>Hap</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compHapIndex</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;">hap</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// hap of new segment</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="java"> <span class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>End</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compHapIndex</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;">modEnd</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// end of old segment</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="java"> <span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateHap</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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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java"> <span class="n" style="color: #333;">head</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateStep</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">step</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;">q</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">offer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">head</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="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">compHapIndex</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="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span></span>
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235
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="java"> <span class="n" style="color: #333;">compositeHapHap</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">compHapIndex</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;">hap</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// hap of new segment</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="java"> <span class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>Hap</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">compHapIndex</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;">hap</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// hap of new segment</span></span>
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<pre style="margin: 0;"> <span id="LC236" 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;">offer</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;">CompHapSegment</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;">step</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">compHapIndex</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -264,8 +264,8 @@ public final class PhaseStates {</td>
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<pre style="margin: 0;"> <span id="LC264" 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;">nCompHaps</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="LC265" 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;">m</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">compHapToEnd</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="LC266" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">compHapToListIndex</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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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compositeHapHap</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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="LC268" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compositeHapEnd</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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="LC267" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>Hap</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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="LC268" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>End</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">refAllele</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;">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;">compHapToHap</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="LC271" 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;">isMissing</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -290,8 +290,8 @@ public final class PhaseStates {</td>
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<pre style="margin: 0;"> <span id="LC290" 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;">nCompositeHaps</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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291
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<pre style="margin: 0;"> <span id="LC291" 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;">m</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">compHapToEnd</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="LC292" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">compHapToListIndex</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="LC293" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compositeHapHap</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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="LC294" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compositeHapEnd</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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="LC293" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>Hap</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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="LC294" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>End</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="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">compHapToListIndex</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="LC295" class="line" lang="java"> <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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">refHap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">compHapToHap</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="LC297" class="line" lang="java"> <span class="n" style="color: #333;">haps</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;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refHap</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -304,10 +304,10 @@ public final class PhaseStates {</td>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC305" 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;">initializeCopy</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;">nSlots</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="LC306" 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;">nSlots</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="LC307" class="line" lang="java"> <span class="n" style="color: #333;">compositeHapEnd</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="na" style="color: #008080;">add</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="c1" style="color: #998; font-style: italic;">// add missing end of last segment</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="java"> <span class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>End</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="na" style="color: #008080;">add</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="c1" style="color: #998; font-style: italic;">// add missing end of last segment</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="java"> <span class="n" style="color: #333;">compHapToListIndex</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 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="LC309" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compositeHapHap</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="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>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compositeHapEnd</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="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>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="java"> <span class="n" style="color: #333;">compHapToHap</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 class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>Hap</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="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>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="java"> <span class="n" style="color: #333;">compHapToEnd</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 class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>End</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="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>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -326,7 +326,7 @@ public final class PhaseStates {</td>
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<pre style="margin: 0;"> <span id="LC326" 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;">h</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;">sample</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="LC327" class="line" lang="java"> <span class="n" style="color: #333;">h</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;">nHaps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="java"> <span class="n" style="color: #333;">compositeHapHap</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="na" style="color: #008080;">size</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;">h</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="java"> <span class="n" style="color: #333;">compositeHap<span class="idiff left right">To</span>Hap</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="na" style="color: #008080;">size</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;">h</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="java"> <span class="n" style="color: #333;">q</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;">new</span> <span class="nc" style="color: #458; font-weight: 600;">CompHapSegment</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;">nMarkers</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/commit/17c4ecf0446518fbdf7063b525bdd875d10535b1#3e06eef3ae51629718f58b9d354c9179c61b3f04"><strong>vcf/AllData.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">@@ -157,7 +157,7 @@ public class AllData implements Data {</td>
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<pre style="margin: 0;"> <span id="LC157" 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;">i</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="LC158" 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;">IntList</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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159
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159
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<pre style="margin: 0;"> <span id="LC159" 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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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nRefSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">re<span class="idiff left">fGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="kc" style="font-weight: 600;"><span class="idiff">null</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">r</span>efGT</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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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nRefSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">re<span class="idiff left">strictRefGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="kc" style="font-weight: 600;"><span class="idiff">null</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">restrictR</span>efGT</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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161
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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;">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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162
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</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;">marker</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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163
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</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;">marker</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -169,8 +169,8 @@ public class AllData implements Data {</td>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="java"> <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="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;">nRefSamples</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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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;">int</span> <span class="n" style="color: #333;">a1</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;">allele1</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;">s</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</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;">allele2</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;">s</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;">int</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re<span class="idiff left right">strictRe</span>fGT</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;">marker</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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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;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re<span class="idiff left right">strictRe</span>fGT</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;">marker</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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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;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</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;">carriers</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">a1</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;">maxCarriers</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;">carriers</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">a1</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;">nTargSamples</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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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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<a href="https://salsa.debian.org/med-team/beagle/commit/17c4ecf0446518fbdf7063b525bdd875d10535b1#78fa00826ae554b25eb82635d04cb923a65a3707"><strong>vcf/BitSetGTRec.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">@@ -89,7 +89,7 @@ public final class BitSetGTRec implements GTRec {</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC90" 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;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isRef</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;">nSamples</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">isPhased</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;">long</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">isMissing</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="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Long</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bitCount</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isPhased</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="nc" style="color: #458; font-weight: 600;"><span class="idiff left">Long</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">SIZE</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="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Long</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">bitCount</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isPhased</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="nc" style="color: #458; font-weight: 600;"><span class="idiff left">Math</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">min</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nSamples</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Long</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">SIZE</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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="LC94" class="line" lang="java"> <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="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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