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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/169b5c18a063266b9cee252aec9e4bcc2cb76671">169b5c18</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2018-09-16T12:01:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.0-180915+dfsg</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#156b60cc697d7e2105fc5f6116490daeacee2f47">
imp/ImputedRecBuilder.java
</a>
</li>
<li class="file-stats">
<a href="#d158c3582076a802a226c9ef95c7781d71642267">
imp/ImputedVcfWriter.java
</a>
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<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
</a>
</li>
<li class="file-stats">
<a href="#960732d02f743e5525a9c84bd179d277e390c9ba">
main/MainHelper.java
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="156b60cc697d7e2105fc5f6116490daeacee2f47">
<a href="https://salsa.debian.org/med-team/beagle/commit/169b5c18a063266b9cee252aec9e4bcc2cb76671#156b60cc697d7e2105fc5f6116490daeacee2f47"><strong>imp/ImputedRecBuilder.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="261" 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">@@ -261,20 +261,27 @@ public final class ImputedRecBuilder {</td>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="java"></span>
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<td class="diff-line-num old_line" data-linenumber="263" 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="263" 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="LC263" 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;">printInfoField</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">PrintWriter</span> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">isImputed</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="LC264" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nAlleles</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"DR2="</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: teal;">comma</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">R2_VALS</span><span class="o" style="font-weight: 600;">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">rint</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">))]);</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="java"> <span class="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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nAlleles</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="269" 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="LC269" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">";AF="</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: teal;">comma</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="270" 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="LC270" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">DF4</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sumAlProbs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">]/</span><span class="n" style="color: #333;">nHaps</span><span class="o" style="font-weight: 600;">));</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</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: teal;">end</span><span class="o" style="font-weight: 600;">()!=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">";END="</span><span class="o" style="font-weight: 600;">);</span></span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</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: teal;">end</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nAlleles</span><span class="o" style="font-weight: 600;">==</span><span class="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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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isImputed</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"IMP"</span><span class="o" style="font-weight: 600;">);</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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275
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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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276
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<pre style="margin: 0;">-<span id="LC276" 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;">isImputed</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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277
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<td class="diff-line-num new_line old" data-linenumber="269" 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="LC277" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">";IMP"</span><span class="o" style="font-weight: 600;">);</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="java"> <span class="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 new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nAlleles</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"DR2="</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: teal;">comma</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">R2_VALS</span><span class="o" style="font-weight: 600;">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">rint</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">100</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">))]);</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nAlleles</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="275" 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">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">";AF="</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: teal;">comma</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">DF4</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">format</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sumAlProbs</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">]/</span><span class="n" style="color: #333;">nHaps</span><span class="o" style="font-weight: 600;">));</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" 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;">marker</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">end</span><span class="o" style="font-weight: 600;">()!=-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">";END="</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</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: teal;">end</span><span class="o" style="font-weight: 600;">());</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" 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;">isImputed</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="java"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">";IMP"</span><span class="o" style="font-weight: 600;">);</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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279
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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280
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="294" 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="301" 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">@@ -294,6 +301,7 @@ public final class ImputedRecBuilder {</td>
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294
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="java"></span>
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295
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302
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<pre style="margin: 0;"> <span id="LC302" 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;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">defaultHomRefFields</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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296
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="java"> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sa</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">5</span><span class="o" style="font-weight: 600;">];</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="java"> <span class="n" style="color: #333;">sa</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tab</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"0|0"</span><span class="o" style="font-weight: 600;">;</span></span>
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297
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="java"> <span class="n" style="color: #333;">sa</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">tab</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"0|0:0"</span><span class="o" style="font-weight: 600;">;</span></span>
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298
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</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;">sa</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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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299
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="java"> <span class="n" style="color: #333;">sa</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;">sa</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="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">",0"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="303" 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="311" 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">@@ -303,7 +311,7 @@ public final class ImputedRecBuilder {</td>
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303
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="java"></span>
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304
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312
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<pre style="margin: 0;"> <span id="LC312" 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;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">homRefFields</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">ap</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">gp</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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305
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<td class="diff-line-num new_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="java"> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">homRefField</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">DEFAULT_HOM_REF_FIELDS</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">];</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nAl</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nAl</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">homRefField</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nAl</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="LC314" 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;">nAl</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">nAl</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">homRefField</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">length</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">nAl</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="LC315" 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 class="n" style="color: #333;">DEFAULT_HOM_REF_FIELDS</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nAl</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ap</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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317
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<pre style="margin: 0;"> <span id="LC317" 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;">a</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;">a</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nAl</span><span class="o" style="font-weight: 600;">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/commit/169b5c18a063266b9cee252aec9e4bcc2cb76671#d158c3582076a802a226c9ef95c7781d71642267"><strong>imp/ImputedVcfWriter.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">@@ -61,7 +61,9 @@ public class ImputedVcfWriter {</td>
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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 refEnd an upper bound (exclusive) on the reference markers</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;"> * that will be printed</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;"> * @throws IndexOutOfBoundsException if</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;"> * {@code (minRefStart < 0 || maxRefEnd > impData.refGT().nMarkers())}</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;"> * {@code (refStart < 0 || refEnd > impData.refGT().nMarkers())}</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;"> * @throws IndexOutOfBoundsException if</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;"> * {@code targCluster < 0 || targCluster >= impData.nClusters()}</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 NullPointerException if {@code impData == null}</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;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">ImputedVcfWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ImpData</span> <span class="n" style="color: #333;">impData</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;">targCluster</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;">refStart</span><span class="o" style="font-weight: 600;">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,18 +78,16 @@ public class ImputedVcfWriter {</td>
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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: teal;">targCluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targCluster</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targCluster</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="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: teal;">refStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refStart</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmpClustEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refStart</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refClusterEnd</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targCluster</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">clustEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpClustEnd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refEnd</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refClusterStart</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targCluster</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;">refEnd</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="java"> <span class="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;">else</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">targCluster</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">impData</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">nClusters</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="java"> <span class="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="LC83" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refStart</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refClusterStart</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targCluster</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targCluster</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">nClusters</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmpClustEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refStart</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refClusterEnd</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targCluster</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">clustEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">tmpClustEnd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">refEnd</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refClusterStart</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targCluster</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;">refEnd</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 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="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: teal;">refStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">max</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">refStart</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">impData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refClusterStart</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">targCluster</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;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">clustEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refEnd</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">refEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refEnd</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="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/commit/169b5c18a063266b9cee252aec9e4bcc2cb76671#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">@@ -70,8 +70,8 @@ public class Main {</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The program name and version.</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="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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<pre style="margin: 0;">-<span id="LC73" 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">03Jul18.40b</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="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">03Jul18.40b</span>.jar"</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="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">15Sep18.8a0</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="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">15Sep18.8a0</span>.jar"</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;"> * 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">@@ -83,7 +83,7 @@ public class Main {</td>
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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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84
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<pre style="margin: 0;"> <span id="LC84" 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: teal;">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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<pre style="margin: 0;"> <span id="LC85" 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: teal;">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: teal;">COPYRIGHT</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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">03Jul18.40b</span>.jar\" to "</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">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">15Sep18.8a0</span>.jar\" to "</span></span>
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<pre style="margin: 0;"> <span id="LC87" 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="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;">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/169b5c18a063266b9cee252aec9e4bcc2cb76671#960732d02f743e5525a9c84bd179d277e390c9ba"><strong>main/MainHelper.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">@@ -101,7 +101,7 @@ public class MainHelper {</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="java"> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">nextLong</span><span class="o" style="font-weight: 600;">());</span></span>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">nanoTime</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="103" 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">
103
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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;">PhaseLS</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">run</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">estPhase</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">recombRegress</span><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;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recombRegress</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="105" 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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104
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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;">recombRegress</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">recombRegress</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: teal;"><span class="idiff">cnt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">()>=</span></span><span class="mi" style="color: #099;"><span class="idiff right">100</span></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_line" data-linenumber="105" 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">
105
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="java"> <span class="n" style="color: #333;">recombFactor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recombFactor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">cd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">recombRegress</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="106" 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">
106
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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>
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<td class="diff-line-num old_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">elapsedNanos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: teal;">nanoTime</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t0</span><span class="o" style="font-weight: 600;">;</span></span>
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