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<h3>
Dylan Aïssi pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/beagle">Debian Med / beagle</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/a65a680954aae0dc8affc42a1072dae6cc093eb5">a65a6809</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-07-04T05:47:34Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.0-190703+dfsg</pre>
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<h4>9 changed files:</h4>
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<li class="file-stats">
<a href="#e1278bf77479ff52b202fca77ce03daef681ef95">
beagleutil/ChromIds.java
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<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
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<li class="file-stats">
<a href="#3e06eef3ae51629718f58b9d354c9179c61b3f04">
vcf/AllData.java
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<li class="file-stats">
<a href="#b4e3e2da9f31a2d4595d94c27b613616b46d12bf">
vcf/RestrictedVcfWindow.java
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<li class="file-stats">
<a href="#3ca7e2987f070ec4990fb9dc5bfc93a9a30c0b2e">
vcf/TargetData.java
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<a href="#de92b0dff67b744e4cd7f4dc81a0eec1299ba200">
vcf/VcfWriter.java
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<a href="#93622cd14d2acecff56306e48fa7fda09fb3ad4b">
<span class="deleted-file">
−
vcf/XBasicGT.java
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−
vcf/XBasicGT1.java
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−
vcf/XGT1.java
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<h4>Changes:</h4>
<li id="e1278bf77479ff52b202fca77ce03daef681ef95">
<a href="https://salsa.debian.org/med-team/beagle/commit/a65a680954aae0dc8affc42a1072dae6cc093eb5#e1278bf77479ff52b202fca77ce03daef681ef95"><strong>beagleutil/ChromIds.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,10 +18,11 @@</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">beagleutil</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.ArrayList</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.List</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.ConcurrentHashMap</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.ConcurrentMap</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.CopyOnWriteArrayList</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>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * <p>Class {@code ChromIds} is a singleton class that represents a</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +39,7 @@ public final class ChromIds {</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ThreadSafeIndexer</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">indexer</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">ConcurrentMap</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Integer</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="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">volatile</span> <span class="n" style="color: #333;"><span class="idiff left right">CopyOnWriteArray</span>List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ids</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">volatile</span> <span class="n" style="color: #333;">List</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ids</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nf" style="color: #900; font-weight: 600;">ChromIds</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// private constructor to restrict instantiation.</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">@@ -46,7 +47,7 @@ public final class ChromIds {</td>
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<pre style="margin: 0;"> <span id="LC47" 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;">indexer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ThreadSafeIndexer</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">initCapacity</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC49" 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;">map</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ConcurrentHashMap</span><span class="o" style="font-weight: 600;"><>(</span><span class="n" style="color: #333;">initCapacity</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;"><span class="idiff left">CopyOnWriteArrayList</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><>(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">String</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC50" 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;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;"><span class="idiff left">ArrayList</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="LC51" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,9 +150,7 @@ public final class ChromIds {</td>
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<pre style="margin: 0;"> <span id="LC150" 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="LC151" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">id</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;">index</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="java"> <span class="k" style="font-weight: 600;">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="n" style="color: #333;">ids</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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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ids</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;">n</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">indexer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="java"> <span class="n" style="color: #333;">ids</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;">indexer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">item</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC154" 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="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">items</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ids</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">);</span></span>
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157
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/commit/a65a680954aae0dc8affc42a1072dae6cc093eb5#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">@@ -68,8 +68,8 @@ public class Main {</td>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The program name and version.</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"(version 5.0)"</span><span class="o" style="font-weight: 600;">;</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.<span class="idiff left right">28Sep18.79</span>3.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.<span class="idiff left right">28Sep18.79</span>3.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <span class="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="n" style="color: #333;">String</span> <span class="n" style="color: #333;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.<span class="idiff left right">03Jul19.b3</span>3.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.<span class="idiff left right">03Jul19.b3</span>3.jar"</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>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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75
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The copyright string.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,7 +81,7 @@ public class Main {</td>
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81
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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82
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">SHORT_HELP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">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="n" style="color: #333;">VERSION</span></span>
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83
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">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="n" style="color: #333;">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="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">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.<span class="idiff left right">28Sep18.79</span>3.jar\" to "</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="n" style="color: #333;">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.<span class="idiff left right">03Jul19.b3</span>3.jar\" to "</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="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="LC86" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Par</span> <span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/commit/a65a680954aae0dc8affc42a1072dae6cc093eb5#3e06eef3ae51629718f58b9d354c9179c61b3f04"><strong>vcf/AllData.java</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,8 +130,7 @@ public class AllData implements Data {</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">GT</span> <span class="nf" style="color: #900; font-weight: 600;">targGTWindow</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Samples</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">GTRec</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">targData</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="n" style="color: #333;">Pedigree</span> <span class="n" style="color: #333;">ped</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="LC133" class="line" lang="java"> <span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BasicGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targData</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;">return</span> <span class="n" style="color: #333;">gt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isGTData</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="n" style="color: #333;">XBasicGT</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="n" style="color: #333;">ped</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>
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<pre style="margin: 0;">+<span id="LC133" 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;">BasicGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targData</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="java"> <span class="nd">@Override</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">@@ -214,8 +213,7 @@ public class AllData implements Data {</td>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">refMarkerIndex</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="java"> <span class="n" style="color: #333;">restricted</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vma</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">refMarkerIndex</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">]];</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java"> <span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BasicGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">restricted</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isGTData</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="n" style="color: #333;">XBasicGT</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="n" style="color: #333;">ped</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>
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<pre style="margin: 0;">+<span id="LC216" 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;">BasicGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">restricted</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="java"></span>
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setRefHaplotypes</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">RefGT</span> <span class="n" style="color: #333;">refGT</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/commit/a65a680954aae0dc8affc42a1072dae6cc093eb5#b4e3e2da9f31a2d4595d94c27b613616b46d12bf"><strong>vcf/RestrictedVcfWindow.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">@@ -98,10 +98,12 @@ public class RestrictedVcfWindow implements Closeable {</td>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fullOverlap</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;">nextMarkers</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;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="java"> <span class="n" style="color: #333;">Marker</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextMarkers</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;">j</span><span class="o" style="font-weight: 600;">);</span></span>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" 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;">next</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;">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;">m</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="o" style="font-weight: 600;">{</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" 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 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;">pos</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="na" style="color: #008080;">pos</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" 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 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;">m</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>
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102
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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="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;">pos</span><span class="o" style="font-weight: 600;">()<</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pos</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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102
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java"> <span class="n" style="color: #333;">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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103
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="k" style="font-weight: 600;">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 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;">pos</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="na" style="color: #008080;">pos</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="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 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;">m</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>
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106
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<pre style="margin: 0;">+<span id="LC106" 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;">pos</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pos</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="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;">equals</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="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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106
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108
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<pre style="margin: 0;"> <span id="LC108" 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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107
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<li id="3ca7e2987f070ec4990fb9dc5bfc93a9a30c0b2e">
<a href="https://salsa.debian.org/med-team/beagle/commit/a65a680954aae0dc8affc42a1072dae6cc093eb5#3ca7e2987f070ec4990fb9dc5bfc93a9a30c0b2e"><strong>vcf/TargetData.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">@@ -88,8 +88,7 @@ public class TargetData implements Data {</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">GT</span> <span class="nf" style="color: #900; font-weight: 600;">targGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Samples</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">GTRec</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">targData</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="java"> <span class="n" style="color: #333;">Pedigree</span> <span class="n" style="color: #333;">ped</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="LC91" class="line" lang="java"> <span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BasicGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targData</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isGTData</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="n" style="color: #333;">XBasicGT</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="n" style="color: #333;">ped</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>
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<pre style="margin: 0;">+<span id="LC91" 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;">BasicGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">targData</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="java"> <span class="nd">@Override</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/commit/a65a680954aae0dc8affc42a1072dae6cc093eb5#de92b0dff67b744e4cd7f4dc81a0eec1299ba200"><strong>vcf/VcfWriter.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">@@ -48,7 +48,7 @@ public final class VcfWriter {</td>
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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="n" style="color: #333;">String</span> <span class="n" style="color: #333;">gtFormat</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=GT,Number=1,Type=String,"</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Description=\"Genotype\">"</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="n" style="color: #333;">String</span> <span class="n" style="color: #333;">dsFormat</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=DS,Number=A,Type=Float,"</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"Description=\"estimated ALT dose [P(RA) + P(AA)]\">"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"Description=\"estimated ALT dose [P(RA) + <span class="idiff left right">2*</span>P(AA)]\">"</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="n" style="color: #333;">String</span> <span class="n" style="color: #333;">ap1Format</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=AP1,Number=A,Type=Float,"</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"Description=\"estimated ALT dose on first haplotype\">"</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;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">String</span> <span class="n" style="color: #333;">ap2Format</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"##FORMAT=<ID=AP2,Number=A,Type=Float,"</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (C) 2014-2016 Brian L. Browning</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Beagle</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Beagle is free software: you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(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="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation, either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Beagle is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">;</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="java"></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">beagleutil.Samples</span><span class="o" style="font-weight: 600;">;</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">blbutil.Const</span><span class="o" style="font-weight: 600;">;</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">main.Pedigree</span><span class="o" style="font-weight: 600;">;</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC25" 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="LC26" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * <p>Class {@code XBasicGT} represents genotype and genotype emission</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * probabilities for a set of samples optimized by sample.</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * </p></span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Instances of class {@code XBasicGTWindow} are immutable.</span></span>
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<pre style="margin: 0;">-<span id="LC30" 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="LC31" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @author Brian L. Browning {@code <browning@uw.edu>}</span></span>
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<pre style="margin: 0;">-<span id="LC32" 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="LC33" 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;">XBasicGT</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="n" style="color: #333;">GT</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Samples</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Markers</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isRefData</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">XBasicGT1</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">gt1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC40" 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="LC41" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Constructs a {@code XBasicGT} instance from the specified data.</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param gl the genotype likelihoods</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param ped the pedigrees</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC46" 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="LC47" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code gl.samples().equals(ped.samples())==false}</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws NullPointerException if {@code gl == null || ped == null}</span></span>
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<pre style="margin: 0;">-<span id="LC49" 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="LC50" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">XBasicGT</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">Pedigree</span> <span class="n" style="color: #333;">ped</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="LC51" 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;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samples</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ped</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samples</span><span class="o" style="font-weight: 600;">())==</span><span class="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="LC52" 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 samples"</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC54" 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;">gl</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="LC55" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">markers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gl</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>
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<pre style="margin: 0;">-<span id="LC56" 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;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samples</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC57" 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;">isRefData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isPhased</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">gt1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">XBasicGT1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nSamples</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC59" 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;">nSamples</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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<pre style="margin: 0;">-<span id="LC60" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">father</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ped</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">father</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mother</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ped</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mother</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"> <span class="n" style="color: #333;">gt1</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 class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">XBasicGT1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gl</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;">father</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">mother</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="java"> <span class="nd">@Override</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="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPhased</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isRefData</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<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="nd">@Override</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="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isGTData</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPhased</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">)</span> <span class="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;">return</span> <span class="n" style="color: #333;">gt1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">isRefSample</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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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="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">gl</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">allele1</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;">allele2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gt1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">gl</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;">allele1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allele2</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPhased</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gt1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">isPhased</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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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC92" 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;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gt1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC97" 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;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gt1</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">allele</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hap</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hap</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">hap</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</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 class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" 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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC113" 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;">nMarkers</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="LC114" 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;">nMarkers</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Marker</span> <span class="nf" style="color: #900; font-weight: 600;">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;">markerIndex</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;">return</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markerIndex</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Markers</span> <span class="nf" style="color: #900; font-weight: 600;">markers</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC128" 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;">nHaps</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="LC129" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">nSamples</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="LC134" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Samples</span> <span class="nf" style="color: #900; font-weight: 600;">samples</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">samples</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="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>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="nd">@Override</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">toString</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="n" style="color: #333;">StringBuilder</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">StringBuilder</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;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"[XBasicGTWindow: nMarkers="</span><span class="o" style="font-weight: 600;">);</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">());</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">" nSamples="</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="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</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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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span><span class="o" style="font-weight: 600;">);</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">();</span> <span class="n" style="color: #333;">m</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;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</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="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MISSING_DATA_CHAR</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// QUAL</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">tab</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"PASS"</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// FILTER</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">tab</span><span class="o" style="font-weight: 600;">);</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MISSING_DATA_CHAR</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// INFO</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">tab</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"GT"</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// FORMAT</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">XGT1</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">gt1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">tab</span><span class="o" style="font-weight: 600;">);</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</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="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>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</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="na" style="color: #008080;">isPhased</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">phasedSep</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">unphasedSep</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="LC164" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</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="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>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span><span class="o" style="font-weight: 600;">);</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">']'</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;">return</span> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">();</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/beagle/commit/a65a680954aae0dc8affc42a1072dae6cc093eb5#b91812813cd21f4a2330ab561508c5e3a0105364"><strong>vcf/XBasicGT1.java</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (C) 2014-2016 Brian L. Browning</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Beagle</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" 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="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Beagle is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation, either version 3 of the License, or</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;">-<span id="LC10" 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="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Beagle is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;">-<span id="LC18" 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="LC19" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">blbutil.Const</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.BitSet</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC24" 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="LC25" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * <p>Class {@code XBasicGT1} represents genotype likelihoods for one sample.</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * </p></span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * <p>Instances of class {@code XBasicGT1} are immutable.</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * </p></span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @author Brian L. Browning {@code <browning@uw.edu>}</span></span>
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<pre style="margin: 0;">-<span id="LC31" 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="LC32" 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;">XBasicGT1</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="n" style="color: #333;">XGT1</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">idIndex</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">Markers</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">BitSet</span> <span class="n" style="color: #333;">missing1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">BitSet</span> <span class="n" style="color: #333;">missing2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">BitSet</span> <span class="n" style="color: #333;">allele1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">BitSet</span> <span class="n" style="color: #333;">allele2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="n" style="color: #333;">BitSet</span> <span class="n" style="color: #333;">isPhased</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isRefSample</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC43" 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="LC44" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Constructs a {@code XBasicGL1} instance from the specified data.</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param gl the genotype likelihoods</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param sample the sample index</span></span>
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<pre style="margin: 0;">-<span id="LC48" 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="LC49" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException if</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code samples < 0 || sample >= gl.nSamples()}</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws NullPointerException if {@code gl == null}</span></span>
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<pre style="margin: 0;">-<span id="LC52" 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="LC53" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">XBasicGT1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">-</span><span 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="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="LC55" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Constructs a {@code XBasicGL1} instance from the specified data.</span></span>
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<pre style="margin: 0;">-<span id="LC59" 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="LC60" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param gt the genotype data</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param sample the sample index</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param father the sample index of the sample's father, or -1 if the</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;"> * father is not genotyped</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;"> * @param mother the sample index of the sample's mother, or -1 if the</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;"> * mother is not genotyped</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="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException 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 samples < 0 || sample >= gl.nSamples()}</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws NullPointerException if {@code gl == null}</span></span>
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<pre style="margin: 0;">-<span id="LC70" 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="LC71" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">XBasicGT1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">gt</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">father</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;">mother</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="LC72" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// NB: phase information in GL is ignored if parental data is used</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nMarkers</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="na" style="color: #008080;">markers</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="LC74" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sumHapBits</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="na" style="color: #008080;">markers</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">sumHaplotypeBits</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">idIndex</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="na" style="color: #008080;">samples</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">idIndex</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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76
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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;">markers</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="na" style="color: #008080;">markers</span><span class="o" style="font-weight: 600;">();</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">missing1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BitSet</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">);</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">missing2</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BitSet</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">);</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele1</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BitSet</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sumHapBits</span><span class="o" style="font-weight: 600;">);</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele2</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BitSet</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sumHapBits</span><span class="o" style="font-weight: 600;">);</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isPhased</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BitSet</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">);</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// // Removing use of pedigree constraints to preserve regression</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// // after changing main.Par.ped() to return pedigree</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// if (father==-1 && mother==-1) {</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// this.isRefSample = copyGL(gl, sample);</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// else {</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// this.isRefSample = useConstraintAndGL(gl, sample, father, mother);</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isRefSample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copyGL</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="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">copyGL</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nMarkers</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;">nMarkers</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"> <span class="n" style="color: #333;">setBits</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;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allele1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">missing1</span><span class="o" style="font-weight: 600;">);</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"> <span class="n" style="color: #333;">setBits</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;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allele2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">missing2</span><span class="o" style="font-weight: 600;">);</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" 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;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isPhased</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="n" style="color: #333;">isPhased</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">);</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <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="o" style="font-weight: 600;">}</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isPhased</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sample</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="o" style="font-weight: 600;">}</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">useConstraintAndGL</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">father</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="LC108" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mother</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nMarkers</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;">nMarkers</span><span class="o" style="font-weight: 600;">();</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">phasedCnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tr1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transmittedAllele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gl</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;">father</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tr2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transmittedAllele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">gl</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;">mother</span><span class="o" style="font-weight: 600;">);</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span><span class="n" style="color: #333;">tr1</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;">tr2</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;">isUnphasedConsistent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tr1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tr2</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="LC117" 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;">isPhasedConsistent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tr1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">tr2</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="LC118" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="java"> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">;</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="o" style="font-weight: 600;">;</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" 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;">tr1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="java"> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr1</span><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="o" style="font-weight: 600;">}</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" 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;">tr2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr2</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">phasedCnt</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="n" style="color: #333;">isPhased</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"> <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;">setBits</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;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allele1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">missing1</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="n" style="color: #333;">setBits</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;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allele2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">missing2</span><span class="o" style="font-weight: 600;">);</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">phasedCnt</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">;</span></span>
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<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>
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139
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<pre style="margin: 0;">-<span id="LC139" 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;">isUnphasedConsistent</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b2</span><span class="o" style="font-weight: 600;">)</span> <span class="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="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">isPhasedConsistent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b2</span><span class="o" style="font-weight: 600;">)</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">isPhasedConsistent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="java"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="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;">isPhasedConsistent</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b2</span><span class="o" style="font-weight: 600;">)</span> <span class="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="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isConsistent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isConsistent</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">b2</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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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="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;">isConsistent</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">b1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC152" 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;">transmittedAllele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">GT</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample</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;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">==-</span><span class="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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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</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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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="java"> <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;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">gl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">:</span> <span class="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>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"></span>
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160
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<pre style="margin: 0;">-<span id="LC160" 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;">setBits</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Markers</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="java"> <span class="n" style="color: #333;">BitSet</span> <span class="n" style="color: #333;">alleles</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">BitSet</span> <span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<pre style="margin: 0;">-<span id="LC162" 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;">allele</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java"> <span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</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="LC164" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
165
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<pre style="margin: 0;">-<span id="LC165" 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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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
166
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<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;">mask</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 old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start</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;">sumHaplotypeBits</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 old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</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;">sumHaplotypeBits</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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;">i</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;">i</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;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mask</span><span class="o" style="font-weight: 600;">)==</span><span class="n" style="color: #333;">mask</span><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="n" style="color: #333;">alleles</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">set</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</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>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="java"> <span class="n" style="color: #333;">mask</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="LC173" class="line" lang="java"> <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="o" style="font-weight: 600;">}</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="java"> <span class="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>
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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">allele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">BitSet</span> <span class="n" style="color: #333;">bitset</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" 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;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sumHaplotypeBits</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 old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</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;">sumHaplotypeBits</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</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 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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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;">bitset</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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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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 class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mask</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 old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">bitset</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="java"> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mask</span><span class="o" style="font-weight: 600;">;</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="java"> <span class="n" style="color: #333;">mask</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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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isRefSample</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="LC196" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isRefSample</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">gl</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">nAlleles</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IndexOutOfBoundsException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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;">a1</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">nAlleles</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IndexOutOfBoundsException</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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;">a2</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">obsA1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">obsA2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">consistent</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">obsA1</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;">obsA1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">obsA2</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;">obsA2</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC210" 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;">consistent</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">false</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isPhased</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;">marker</span><span class="o" style="font-weight: 600;">)==</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="java"> <span class="n" style="color: #333;">consistent</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">obsA1</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;">obsA1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">obsA2</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;">obsA2</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">);</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">consistent</span> <span class="o" style="font-weight: 600;">?</span> <span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">:</span> <span class="mf" style="color: #099;">0.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPhased</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">isPhased</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;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC222" 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;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">missing1</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;">marker</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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">allele1</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC227" 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;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">missing2</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;">marker</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="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">allele</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">allele2</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC232" 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;">nMarkers</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="LC233" 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;">nMarkers</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Marker</span> <span class="nf" style="color: #900; font-weight: 600;">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;">markerIndex</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="LC238" 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;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markerIndex</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">Markers</span> <span class="nf" style="color: #900; font-weight: 600;">markers</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC247" 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;">idIndex</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="LC248" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">idIndex</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">toString</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="LC253" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nMarkers</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;">nMarkers</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="java"> <span class="n" style="color: #333;">StringBuilder</span> <span class="n" style="color: #333;">sb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">StringBuilder</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"[XBasicGL1: nMarkers="</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span><span class="o" style="font-weight: 600;">);</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nMarkers</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markers</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">tab</span><span class="o" style="font-weight: 600;">);</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isPhased</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">phasedSep</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">unphasedSep</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">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>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="java"> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="sc" style="color: #d14;">']'</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">();</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/beagle/commit/a65a680954aae0dc8affc42a1072dae6cc093eb5#d8b658ede0edaba477f0f9a3fbd2de6136ee7448"><strong>vcf/XGT1.java</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (C) 2014-2016 Brian L. Browning</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Beagle</span></span>
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<pre style="margin: 0;">-<span id="LC5" 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="LC6" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Beagle is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation, either version 3 of the License, or</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;">-<span id="LC10" 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="LC11" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Beagle is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;">-<span id="LC18" 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="LC19" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// Later consider relaxing mutability, and determine whether interface</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// can be replaced with implementing class</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC24" 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="LC25" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * <p>Interface {@code XGT1} (Genotype Likelihoods) represents genotype</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * likelihoods for one sample.</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * </p></span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * <p>Instances of {@code XGT1} are required to be immutable.</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * </p></span></span>
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<pre style="margin: 0;">-<span id="LC30" 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="LC31" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @author Brian L. Browning {@code <browning@uw.edu>}</span></span>
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<pre style="margin: 0;">-<span id="LC32" 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="LC33" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">interface</span> <span class="nc" style="color: #458; font-weight: 600;">XGT1</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC35" 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="LC36" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns {@code true} if the observed data for each marker</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * includes a phased genotype that has no missing alleles,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * and returns {@code false} otherwise.</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return {@code true} if the observed data for each marker</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * includes a phased genotype that has no missing alleles,</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * and {@code false} otherwise</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isRefSample</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC45" 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="LC46" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the probability of the observed data for the specified marker</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * if the specified pair of ordered alleles is the true ordered genotype.</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param marker the marker index</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param allele1 the first allele index</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param allele2 the second allele index</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the probability of the observed data for the specified marker</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * and sample if the specified pair of ordered alleles is the true</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * ordered genotype</span></span>
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<pre style="margin: 0;">-<span id="LC54" 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="LC55" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException if</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code marker < 0 || marker >= this.nMarkers()}</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException if</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code allele1 < 0 || allele1 >= this.marker(marker).nAlleles()}</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException if</span></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;"> * {@code allele2 < 0 || allele2 >= this.marker(marker).nAlleles()}</span></span>
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<pre style="margin: 0;">-<span id="LC61" 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="LC62" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">gl</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">allele1</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;">allele2</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns {@code true} if the observed data for the specified</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;"> * marker includes a phased genotype, and returns {@code false} otherwise.</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;"> * @param marker the marker index</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;"> * @return {@code true} if the observed data for the specified</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * marker includes a phased genotype, and {@code false} otherwise</span></span>
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<pre style="margin: 0;">-<span id="LC70" 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="LC71" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException 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 marker < 0 || marker >= this.nMarkers()}</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="LC74" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">isPhased</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the first allele for the specified marker if the observed data</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * include a non-missing allele, and returns -1 otherwise. Alleles are</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * arbitrarily ordered if the genotype is unphased.</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param marker the marker index</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the first allele for the specified marker if the observed data</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * include a non-missing allele, and -1 otherwise</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException if</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code marker < 0 || marker >= this.nMarkers()}</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC89" 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="LC90" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the second allele for the specified marker if the observed data</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * include a non-missing allele, and returns -1 otherwise. Alleles are</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * arbitrarily ordered if the genotype is unphased.</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param marker the marker index</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the second allele for the specified marker if the observed data</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * include a non-missing allele, and -1 otherwise</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException if</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code marker < 0 || marker >= this.nMarkers()}</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the number of markers.</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the number of markers</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">nMarkers</span><span class="o" style="font-weight: 600;">();</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the specified marker.</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param marker the marker index</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the specified marker</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @throws IndexOutOfBoundsException if</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code marker < 0 || marker >= this.nMarkers()}</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"> <span class="n" style="color: #333;">Marker</span> <span class="nf" style="color: #900; font-weight: 600;">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;">marker</span><span class="o" style="font-weight: 600;">);</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="java"></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the list of markers.</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the list of markers</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="java"> <span class="n" style="color: #333;">Markers</span> <span class="nf" style="color: #900; font-weight: 600;">markers</span><span class="o" style="font-weight: 600;">();</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="java"></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the sample identifier index.</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the sample identifier index</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">idIndex</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="java"></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns a string representation of {@code this}. The exact</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * details of the representation are unspecified and subject to change.</span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return a string representation of {@code this}</span></span>
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<pre style="margin: 0;">-<span id="LC133" 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="LC134" class="line" lang="java"> <span class="nd">@Override</span></span>
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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="java"> <span class="n" style="color: #333;">String</span> <span class="nf" style="color: #900; font-weight: 600;">toString</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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