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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/32b96745d1405627d139e59191f7108d2f79f40f">32b96745</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-12-14T17:58:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.1-191125+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/48f79ba956e68a83da81ce02e1569537970b2550">48f79ba9</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-12-14T17:58:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.1-191125+dfsg'
Update to upstream version '5.1-191125+dfsg'
with Debian dir fadb450493679840ab428de2b98448b709c7a3a2</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
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<li class="file-stats">
<a href="#6ba560a119d50b4bdbe6c09549cb4a9204ac0f16">
vcf/PlinkGenMap.java
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<li class="file-stats">
<a href="#c551c47ccd8315bcb63f95e39091771553cb34f3">
vcf/WindowIt.java
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<h4>Changes:</h4>
<li id="2ad0efaccf66628e1858a4c133e8914e33eb2221">
<a href="https://salsa.debian.org/med-team/beagle/compare/4d7d5a3810956f435be1cea8a9ca0260b9003170...48f79ba956e68a83da81ce02e1569537970b2550#2ad0efaccf66628e1858a4c133e8914e33eb2221"><strong>main/Main.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,8 +65,8 @@ public class Main {</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The program name and version.</span></span>
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<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">0Nov19.573</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.2<span class="idiff left right">0Nov19.573</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">5Nov19.28d</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.2<span class="idiff left right">5Nov19.28d</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">0Nov19.573</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">5Nov19.28d</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/4d7d5a3810956f435be1cea8a9ca0260b9003170...48f79ba956e68a83da81ce02e1569537970b2550#6ba560a119d50b4bdbe6c09549cb4a9204ac0f16"><strong>vcf/PlinkGenMap.java</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -307,11 +307,11 @@ public final class PlinkGenMap implements GeneticMap {</td>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;"> <span id="LC309" 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;">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;">chrom</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;">basePosition</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="LC310" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minEndCm</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">5.0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="java"> <span class="n" style="color: #333;">checkChromIndex</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mapSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="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="LC313" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mapSize</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">mapSize</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">minEndCmDist</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">5.0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mapSizeM1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="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="LC313" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="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;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">basePosition</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">>=</span><span 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="LC317" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">index</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="319" style="width: 35px; color: rgba(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="319" style="width: 35px; color: rgba(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">@@ -319,23 +319,23 @@ public final class PlinkGenMap implements GeneticMap {</td>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">index</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="LC320" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">aIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">insPt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="n" style="color: #333;"><span class="idiff right">mapSize</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="LC323" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">mapSize</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">minEndCm</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">aIndex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="n" style="color: #333;"><span class="idiff right">mapSizeM1</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="LC323" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">mapSize<span class="idiff left">M1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">minEndCmDist</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;"><<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">mapSize</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left right">mapSizeM1</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="java"> <span class="n" style="color: #333;">aIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="java"> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapSize</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-</span></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="LC329" class="line" lang="java"> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapSize<span class="idiff left right">M</span>1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="java"> <span class="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;"><span class="idiff left right">insPt</span></span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">minEndCm</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="java"> <span class="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;"><span class="idiff left right">bIndex</span></span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">minEndCm<span class="idiff left right">Dist</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="java"> <span class="n" style="color: #333;">aIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="java"> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mapSize</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-</span></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="LC338" class="line" lang="java"> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mapSize<span class="idiff left right">M</span>1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePosition</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -349,30 +349,46 @@ public final class PlinkGenMap implements GeneticMap {</td>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">basePos</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">geneticPosition</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="java"> <span class="n" style="color: #333;">checkChromIndex</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minEndBasepairDist</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5_000_000</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mapSizeM1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="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;">chrom</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">geneticPosition</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC357" 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;">index</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">index</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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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="java"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">]==</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="java"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">aIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">minEndBasepairDist</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="java"> <span class="n" style="color: #333;">aIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="java"> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">;</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">]==</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="java"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">;</span></span>
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363
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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364
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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365
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<pre style="margin: 0;">-<span id="LC365" 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;">insPt</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">;</span></span>
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367
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">]==</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">])</span> <span class="o" style="font-weight: 600;">{</span></span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">;</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">minEndBasepairDist</span><span class="o" style="font-weight: 600;">);</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="java"> <span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">insPt</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="java"> <span class="n" style="color: #333;">aIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="java"> <span class="n" style="color: #333;">bIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">insPt</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="java"> <span class="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">aIndex</span><span class="o" style="font-weight: 600;">]==</span><span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mapSizeM1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bIndex</span><span class="o" style="font-weight: 600;">;</span></span>
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369
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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370
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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371
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">geneticPosition</span><span class="o" style="font-weight: 600;">;</span></span>
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372
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<td class="diff-line-num new_line old" data-linenumber="388" style="width: 35px; color: rgba(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="LC372" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left">insPt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="o" style="font-weight: 600;">];</span></span>
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373
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<td class="diff-line-num new_line old" data-linenumber="388" style="width: 35px; color: rgba(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="LC373" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left right">insPt</span></span><span class="o" style="font-weight: 600;">];</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left">insPt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="o" style="font-weight: 600;">];</span></span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left right">insPt</span></span><span class="o" style="font-weight: 600;">];</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left right">aIndex</span></span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genPos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left right">bIndex</span></span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left right">aIndex</span></span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">basePos</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">chrom</span><span class="o" style="font-weight: 600;">][</span><span class="n" style="color: #333;"><span class="idiff left right">bIndex</span></span><span class="o" style="font-weight: 600;">];</span></span>
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376
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<td class="diff-line-num new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">interp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">)/(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fb</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">);</span></span>
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377
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">interp</span><span class="o" style="font-weight: 600;">>=</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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378
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<td class="diff-line-num new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Base position exceeds Integer.MAX_VALUE"</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/compare/4d7d5a3810956f435be1cea8a9ca0260b9003170...48f79ba956e68a83da81ce02e1569537970b2550#c551c47ccd8315bcb63f95e39091771553cb34f3"><strong>vcf/WindowIt.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="260" style="width: 35px; color: rgba(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">@@ -260,7 +260,7 @@ public class WindowIt<E extends GTRec> implements SampleFileIt<Window<E>> {</td>
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260
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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261
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">endPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genMap</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">basePos</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">chromIndex</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">endCm</span><span class="o" style="font-weight: 600;">);</span></span>
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262
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">overlapEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextList</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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<td class="diff-line-num old old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="java"> <span class="n" style="color: #333;">nextList</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;">next</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// ensure at least on record is added</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="java"> <span class="n" style="color: #333;">nextList</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;">next</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// ensure at least on<span class="idiff left right">e</span> record is added</span></span>
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<td class="diff-line-num old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
264
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="java"> <span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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265
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<td class="diff-line-num new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC265" 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;">next</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span></span>
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<td class="diff-line-num old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">next</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="na" style="color: #008080;">chromIndex</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">chromIndex</span></span>
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