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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/beagle">Debian Med / beagle</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/dcb39a5143ebd41a68edcb1a51902776b6b28079">dcb39a51</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-04-30T08:23:15+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.1-200427+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/432395f9e343195519646b18faf3a979c40f3578">432395f9</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2020-04-30T08:23:16+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.1-200427+dfsg'
Update to upstream version '5.1-200427+dfsg'
with Debian dir 4f736ae48482b32679e502335b8bff60f6f60c22</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
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<li class="file-stats">
<a href="#07777d8f0265190c58c0ca3fad4559f401a7fd13">
phase/FixedPhaseData.java
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<li class="file-stats">
<a href="#bff5675255d46d340fc57b49cdb9d933b6ba9ad4">
phase/Ibs2.java
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<h4>Changes:</h4>
<li id="2ad0efaccf66628e1858a4c133e8914e33eb2221">
<a href="https://salsa.debian.org/med-team/beagle/-/compare/3dae6444af2832690b1c5df6e46f1437d30f8e69...432395f9e343195519646b18faf3a979c40f3578#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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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"(version 5.1)"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.2<span class="idiff left right">4Mar20.5f5</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">4Mar20.5f5</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.2<span class="idiff left right">7Apr20.b81</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">7Apr20.b81</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The copyright string.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,7 +78,7 @@ public class Main {</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">SHORT_HELP</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">VERSION</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">COPYRIGHT</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Enter \"java -jar beagle.2<span class="idiff left right">4Mar20.5f5</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">7Apr20.b81</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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<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/-/compare/3dae6444af2832690b1c5df6e46f1437d30f8e69...432395f9e343195519646b18faf3a979c40f3578#07777d8f0265190c58c0ca3fad4559f401a7fd13"><strong>phase/FixedPhaseData.java</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +46,6 @@ import vcf.SplicedGT;</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FixedPhaseData</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>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">MAX_HIFREQ_PROP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.9f</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;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">MIN_IBS2_CM</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="java"> <span class="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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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">err</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">@@ -145,7 +144,7 @@ public class FixedPhaseData {</td>
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<pre style="margin: 0;"> <span id="LC144" 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;">prevHiFreqMarker</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prevHiFreqMarker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nMarkers</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">hiFreqIndices</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</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;">prevWt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hiFreqIndices</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ibs2</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;">Ibs2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hiFreqTargGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hiFreqRefGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hiFreqMap</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff right">MIN_IBS2_CM</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ibs2</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;">Ibs2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">hiFreqTargGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hiFreqRefGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">hiFreqMap</span><span class="o" style="font-weight: 600;">);</span></span>
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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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<pre style="margin: 0;"> <span id="LC149" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ignoreLowFreqCarriers</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">IntArray</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="o" style="font-weight: 600;">{</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/compare/3dae6444af2832690b1c5df6e46f1437d30f8e69...432395f9e343195519646b18faf3a979c40f3578#bff5675255d46d340fc57b49cdb9d933b6ba9ad4"><strong>phase/Ibs2.java</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,6 +25,7 @@ import ints.WrappedIntArray;</td>
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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;">java.util.ArrayList</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;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.List</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Random</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.function.Predicate</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.stream.Collectors</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.stream.IntStream</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">@@ -43,15 +44,17 @@ import vcf.RefGT;</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Ibs2</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MIN_STEP_MARKERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">;</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_STEP_MARKERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1500</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// high-frequency markers</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">MAX_MISS_PROP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.1f</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">MIN_IBS2_CM</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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49
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="no" style="color: #008080;">MAX_IBD_GAP_CM</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">4.0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">MAX_MISS_FREQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.1f</span><span class="o" style="font-weight: 600;">;</span></span>
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<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;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">MIN_MINOR_FREQ</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.02f</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;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">MIN_STEP_CM</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.5f</span><span class="o" style="font-weight: 600;">*</span><span class="no" style="color: #008080;">MIN_IBS2_CM</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;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MIN_STEP_MARKERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">MAX_STEP_MARKERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">;</span></span>
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<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="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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<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;">DoubleArray</span> <span class="n" style="color: #333;">genPos</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;">double</span> <span class="n" style="color: #333;">minCmIbs2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">SampleSeg</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">sampleSegs</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">// [targ sample][segment]</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC60" 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="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,7 +63,6 @@ public final class Ibs2 {</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param refGT the reference genotype data or {@code null} if there are</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * no reference data</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param map an array with the genetic map positions of each marker</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param minCmIbs2 the minimum cM length of a stored IBS2 segment</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;"> * @throws NullPointerException if {@code (targGT == null || map == null)}</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IllegalArgumentException if</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code targGT.nMarkers() != map.genPos().size()}</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">@@ -69,22 +71,23 @@ public final class Ibs2 {</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IllegalArgumentException if</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code (minCmIbs2 <= 0 || Double.isFinite(minCmIbs2) == false)}</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">Ibs2</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">MarkerMap</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">minCmIbs2</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="n" style="color: #333;">checkArgs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">minCmIbs2</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">Ibs2</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">MarkerMap</span> <span class="n" style="color: #333;">map</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="LC75" class="line" lang="java"> <span class="n" style="color: #333;">checkArgs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">map</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;">targGT</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>
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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;">refGT</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>
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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;">genPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">genPos</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;">minCmIbs2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minCmIbs2</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="nc" style="color: #458; font-weight: 600;">IntArray</span> <span class="n" style="color: #333;">windowStarts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stepStarts</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">,</span> <span class="mf" style="color: #099;">0.5</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">minCmIbs2</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="nc" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">useMarker</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">useMarker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targGT</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>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntArray</span> <span class="n" style="color: #333;">windowStarts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stepStarts</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">useMarker</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC83" 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;">idSets</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;">windowStarts</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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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parallel</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">-<span id="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;">w</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">ibsSamples</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">windowStarts</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;">+<span id="LC85" 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;">w</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">ibsSamples</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">useMarker</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">windowStarts</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">))</span></span>
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83
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<pre style="margin: 0;"> <span id="LC86" 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="kt" style="color: #458; font-weight: 600;">int</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 class="c1" style="color: #998; font-style: italic;">//[window][targ_sample][ibs2_samples]</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nMarkersM1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nMarkers</span><span class="o" style="font-weight: 600;">()</span> <span 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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86
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Predicate</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">SampleSeg</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">predicate</span> <span class="o" style="font-weight: 600;">=</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">-></span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">inclEnd</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">start</span><span class="o" style="font-weight: 600;">()))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;"><span class="idiff left right">minCmIbs2</span></span><span class="o" style="font-weight: 600;">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="java"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">-></span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">inclEnd</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">start</span><span class="o" style="font-weight: 600;">()))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="no" style="color: #008080;"><span class="idiff left right">MIN_IBS2_CM</span></span><span class="o" style="font-weight: 600;">;</span></span>
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88
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91
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<pre style="margin: 0;"> <span id="LC91" 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;">sampleSegs</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;">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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89
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parallel</span><span class="o" style="font-weight: 600;">()</span></span>
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90
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<pre style="margin: 0;"> <span id="LC93" 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;">s</span> <span class="o" style="font-weight: 600;">-></span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -99,95 +102,98 @@ public final class Ibs2 {</td>
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99
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<pre style="margin: 0;"> <span id="LC102" 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;">SampleSeg</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="LC103" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">checkArgs</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">MarkerMap</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">,</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minIbs2Cm</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">checkArgs</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">MarkerMap</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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104
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nMarkers</span><span class="o" style="font-weight: 600;">()!=</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">genPos</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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105
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="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;">map</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">genPos</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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106
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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107
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<pre style="margin: 0;"> <span id="LC109" 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;">refGT</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">markers</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">equals</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;">markers</span><span class="o" style="font-weight: 600;">())==</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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108
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"inconsistent markers"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC110" 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;">minIbs2Cm</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;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFinite</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">minIbs2Cm</span><span class="o" style="font-weight: 600;">)==</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="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;">minIbs2Cm</span><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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">IntArray</span> <span class="nf" style="color: #900; font-weight: 600;">stepStarts</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">MarkerMap</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">map</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">minCM</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="LC116" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">genPos</span></span><span class="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">map</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">genPos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">().</span></span><span class="na" style="color: #008080;"><span class="idiff right">toArray</span></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="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">indices</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left right">length</span></span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">IntArray</span> <span class="nf" style="color: #900; font-weight: 600;">stepStarts</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">Boolean</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[]</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">useMarker</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">MarkerMap</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">map</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="LC115" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">DoubleArray</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">genPos</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">map</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">genPos</span></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="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">indices</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left">size</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>/</span><span class="mi" style="color: #099;">100</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="LC117" class="line" lang="java"></span>
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119
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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;">nextStart</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="LC120" 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;">nextStart</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left right">length</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="LC119" 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;">nextStart</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left">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="LC120" class="line" lang="java"> <span class="n" style="color: #333;">indices</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;">nextStart</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">nextStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextStart</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">nextStart</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">min</span>CM</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;">nextStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextStart</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">useMarker</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nextStart</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff right">MIN_STEP_</span>CM</span><span class="o" style="font-weight: 600;">);</span></span>
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123
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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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124
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<pre style="margin: 0;">-<span id="LC124" 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;">popLastInterval</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indices</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">minCM</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nextStart</span><span class="o" style="font-weight: 600;">==</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// last interval is too short and should be removed</span></span>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="java"> <span class="n" style="color: #333;">indices</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pop</span><span class="o" style="font-weight: 600;">();</span></span>
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126
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">WrappedIntArray</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indices</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="na" style="color: #008080;"><span class="idiff">toArray</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>);</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">WrappedIntArray</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indices</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">nextStart</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">genPos</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;">double</span> <span class="n" style="color: #333;">minCM</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">nextGenPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">minCM</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nextIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</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;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="java"> <span class="n" style="color: #333;">nextGenPos</span><span class="o" style="font-weight: 600;">);</span></span>
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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;">nextIndex</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> <span class="n" style="color: #333;">nextIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nextIndex</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="LC130" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">nextStart</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">DoubleArray</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">useMarker</span><span class="o" style="font-weight: 600;">,</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minCM</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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<pre style="margin: 0;">+<span id="LC132" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nextStart</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">markerCnt</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="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" 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;">nextStart</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">useMarker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">markerCnt</span><span class="o" style="font-weight: 600;"><</span><span class="no" style="color: #008080;">MIN_STEP_MARKERS</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="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" 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;">useMarker</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nextStart</span><span class="o" style="font-weight: 600;">])</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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">markerCnt</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="o" style="font-weight: 600;">}</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nextStart</span><span class="o" style="font-weight: 600;">;</span></span>
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136
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nextStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextIndex</span><span class="o" style="font-weight: 600;">;</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minNextStart</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="no" style="color: #008080;">MIN_STEP_MARKERS</span><span class="o" style="font-weight: 600;">;</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxNextStart</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="no" style="color: #008080;">MAX_STEP_MARKERS</span><span class="o" style="font-weight: 600;">;</span></span>
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141
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<td class="diff-line-num new_line old" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC141" 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;">nextStart</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">minNextStart</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="n" style="color: #333;">nextStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minNextStart</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">targCM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">minCM</span><span class="o" style="font-weight: 600;">;</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" 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;">nextStart</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">useMarker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nextStart</span><span class="o" style="font-weight: 600;">)<</span><span class="n" style="color: #333;">targCM</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">markerCnt</span><span class="o" style="font-weight: 600;"><</span><span class="no" style="color: #008080;">MAX_STEP_MARKERS</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">useMarker</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nextStart</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">markerCnt</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nextStart</span><span class="o" style="font-weight: 600;">;</span></span>
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143
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nextStart</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxNextStart</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"> <span class="n" style="color: #333;">nextStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxNextStart</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nextStart</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">useMarker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">&&</span></span>
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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 class="n" style="color: #333;">markerCnt</span><span class="o" style="font-weight: 600;"><</span><span class="no" style="color: #008080;">MIN_STEP_MARKERS</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nextStart</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;">targCM</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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<pre style="margin: 0;">+<span id="LC150" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// signal that last interval is too short and should be removed</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="java"> <span class="n" style="color: #333;">nextStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nextStart</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC150" 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;">popLastInterval</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">indices</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">,</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minCM</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">indices</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span 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="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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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <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;">else</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;">lastStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indices</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;">indices</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lastStart</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="no" style="color: #008080;">MIN_STEP_MARKERS</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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158
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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="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">lastStart</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;">0.5</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">minCM</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[][]</span> <span class="nf" style="color: #900; font-weight: 600;">ibsSamples</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">IntArray</span> <span class="n" style="color: #333;">wStarts</span><span class="o" style="font-weight: 600;">,</span></span>
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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;">w</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="c1" style="color: #998; font-style: italic;">// To Do: ibsSamples need to be updated to incorporate useMarker</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[][]</span> <span class="nf" style="color: #900; font-weight: 600;">ibsSamples</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">useMarker</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="nc" style="color: #458; font-weight: 600;">IntArray</span> <span class="n" style="color: #333;">wStarts</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;">w</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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164
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">wP1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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165
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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;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">);</span></span>
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166
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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;">int</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">wP1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">wStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">wStarts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">wP1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nMarkers</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC162" 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;">markers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">useMarker</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;">end</span><span class="o" style="font-weight: 600;">);</span></span>
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167
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">SampClust</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">equivLists</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span><span class="o" style="font-weight: 600;"><>(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> <span class="n" style="color: #333;">equivLists</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">initCluster</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">end</span></span><span class="o" style="font-weight: 600;">));</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff right">m</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="LC164" class="line" lang="java"> <span class="n" style="color: #333;">equivLists</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">initCluster</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left right">markers</span></span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">markers</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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170
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">;</span></span>
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171
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="java"> <span class="n" style="color: #333;">equivLists</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">equivLists</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stream</span><span class="o" style="font-weight: 600;">()</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">flatMap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">ia</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">partition</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">targGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ia</span></span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mm</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">flatMap</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">list</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">partition</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">targGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">refGT</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">list</span></span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mm</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">collect</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Collectors</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toCollection</span><span class="o" style="font-weight: 600;">(</span><span class="nl">ArrayList:</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="LC170" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">results</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">equivLists</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="java"></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">SampClust</span> <span class="nf" style="color: #900; font-weight: 600;">initCluster</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">,</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">markers</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">useMarker</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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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IntList</span> <span class="n" style="color: #333;">markers</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="no" style="color: #008080;">MIN_STEP_MARKERS</span><span class="o" style="font-weight: 600;">);</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="java"> <span class="k" style="font-weight: 600;">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="LC177" 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;">useMarker</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="LC178" class="line" lang="java"> <span class="n" style="color: #333;">markers</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;">m</span><span class="o" style="font-weight: 600;">);</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java"> <span class="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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">();</span></span>
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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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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="java"></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">SampClust</span> <span class="nf" style="color: #900; font-weight: 600;">initCluster</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span></span>
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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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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180
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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;">int</span> <span class="n" style="color: #333;">nTargSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">();</span></span>
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181
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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;">int</span> <span class="n" style="color: #333;">nSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMiss</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ceil</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">MAX_MISS_PROP</span><span class="o" style="font-weight: 600;">*(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">));</span></span>
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183
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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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">missCnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nSamples</span><span class="o" style="font-weight: 600;">];</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">;</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff right">m</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" 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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">markers</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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185
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190
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<pre style="margin: 0;"> <span id="LC190" 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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186
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">)==-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">)==-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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187
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">missCnt</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">];</span></span>
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188
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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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189
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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 class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMiss</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ceil</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">MAX_MISS_FREQ</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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191
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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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">initCluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">IntStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">range</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">nSamples</span><span class="o" style="font-weight: 600;">)</span></span>
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192
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">filter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">nTargSamples</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">missCnt</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">]<=</span><span class="n" style="color: #333;">maxMiss</span><span class="o" style="font-weight: 600;">)</span></span>
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -221,9 +227,10 @@ public final class Ibs2 {</td>
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221
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nTargSamples</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">missingTargSamples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">// assumes int[] parent.samples is increasing</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="java"> <span class="n" style="color: #333;">gtIndices</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="java"> <span class="n" style="color: #333;">areHom</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">areHomozygous</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gt</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;">gt</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="LC230" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// put s and missTargSamples in new list</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// s MUST come after missing target samples for list to be increasing</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="java"> <span class="n" style="color: #333;">gtToList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">IntList</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">missingTargSamples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// if s>=nTargSamples, put s in list w/ missTargSamples</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="java"> <span class="n" style="color: #333;">gtToList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">missingTargSamples</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;">k</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="java"> <span class="n" style="color: #333;">gtToList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">gtIndex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -403,14 +410,6 @@ public final class Ibs2 {</td>
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403
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC406" 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="LC407" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the minimum cM length of a stored IBS2 segment.</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the minimum cM length of a stored IBS2 segment</span></span>
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<pre style="margin: 0;">-<span id="LC409" 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="LC410" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">minCmIbs2</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="LC411" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">minCmIbs2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC413" 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="LC414" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns {@code true} if the specified samples are estimated</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * to be IBS2 at the specified marker, and the IBS2 interval</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">@@ -463,4 +462,58 @@ public final class Ibs2 {</td>
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<pre style="margin: 0;"> <span id="LC462" 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;">areHomozygous</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">useMarker</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</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="LC467" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minTotalHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">200</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC468" 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;">refHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refHaps</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">minTotalHaps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="java"> <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 class="n" style="color: #333;">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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<pre style="margin: 0;">+<span id="LC470" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxMiss</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">MAX_MISS_FREQ</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="LC471" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minMinor</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">round</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">MIN_MINOR_FREQ</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="n" style="color: #333;">refHaps</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">));</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nMarkers</span><span class="o" style="font-weight: 600;">())</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parallel</span><span class="o" style="font-weight: 600;">()</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" 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;">m</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">accept</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refHaps</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maxMiss</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">minMinor</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;">+<span id="LC475" 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;">Boolean</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="LC476" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="java"></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">refHaps</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</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;">minTotalHaps</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="LC479" class="line" lang="java"> <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 class="n" style="color: #333;">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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<pre style="margin: 0;">+<span id="LC480" 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;">refGT</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">minTotalHaps</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="LC481" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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;">0</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">xtraRefHaps</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;">minTotalHaps</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="n" style="color: #333;">refGT</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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484
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<pre style="margin: 0;">+<span id="LC484" 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;">xtraRefHaps</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;">nHaps</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" 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;">xtraRefHaps</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ints</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">xtraRefHaps</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;">refGT</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="na" style="color: #008080;">sorted</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">();</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" 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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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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;">refGT</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="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">();</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="java"></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">Boolean</span> <span class="nf" style="color: #900; font-weight: 600;">accept</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">refHaps</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="java"> <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;">maxMiss</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;">minMinor</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="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
495
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<pre style="margin: 0;">+<span id="LC495" 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;">cnts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">missAndAlleleCnts</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refHaps</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
496
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<pre style="margin: 0;">+<span id="LC496" 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;">cnts</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;">maxMiss</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cnts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">Boolean</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">FALSE</span><span class="o" style="font-weight: 600;">;</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cnts</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;">cnts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">Boolean</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;">cnts</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">cnts</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minMinor</span><span class="o" style="font-weight: 600;">);</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="java"></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">missAndAlleleCnts</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">refHaps</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">GT</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">,</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="java"> <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="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">equals</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;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">));</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nAllelesP1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targGT</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">nAlleles</span><span class="o" style="font-weight: 600;">()</span> <span 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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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// missing allele cnt is in element [0], ref allele cnt is in element [1]</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" 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;">cnts</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;">nAllelesP1</span><span class="o" style="font-weight: 600;">];</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" 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;">refGT</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" 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;">refHap</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">refHaps</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">cnts</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;">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;">refHap</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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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" 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;">h</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;">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 class="n" style="color: #333;">h</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;">h</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="LC515" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">cnts</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;">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;">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>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cnts</span><span class="o" style="font-weight: 600;">;</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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