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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/beagle">Debian Med / beagle</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/3b5c416420dfba1f3b20402e52d8c90a5f13e89d">3b5c4164</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T17:19:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 220208</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/9647394404dc64fcde692045300f873ced95cb75">96473944</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T17:19:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/a25f979e028520551c519dda963288f50096f1bc">a25f979e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T17:19:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/220208'
Update to upstream version '220208'
with Debian dir 625888870304b0f6fc6e5d891bf89842feaed6e2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/b063ef8d6ad722145798fd153daa3f2bc86e3e7b">b063ef8d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T17:19:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/a8e5fbe0c92e879bb47772d921f94a1072423b5c">a8e5fbe0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T17:21:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#88c53e80182ef20a8cdfed427d5e651d37907e75">
bref/Bref3.java
</a>
</li>
<li class="file-stats">
<a href="#dcb0e12a67291331c7d1fd8dd651714b291527c8">
bref/UnBref3.java
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
</a>
</li>
<li class="file-stats">
<a href="#eb9d1a1acbc4ec0ffa4eeee52a6d83ce5c15c2e1">
main/Par.java
</a>
</li>
<li class="file-stats">
<a href="#611062e8e142f9ef1d5f5200bb13b0a16611898e">
main/RunStats.java
</a>
</li>
<li class="file-stats">
<a href="#4321c8a41eba5c2d331cb0edb16f56f6fb705039">
phase/HmmParamData.java
</a>
</li>
<li class="file-stats">
<a href="#4af4ff2035566714b46668721223bba4a04beaf0">
phase/ParamEstimates.java
</a>
</li>
<li class="file-stats">
<a href="#feb7a9a924cfaa0b13e7c2647499887d74f2b2bb">
phase/PhaseData.java
</a>
</li>
<li class="file-stats">
<a href="#d0875a14cecab64969d49fa0ec30b89961d311ed">
phase/PhaseLS.java
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="88c53e80182ef20a8cdfed427d5e651d37907e75">
<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#88c53e80182ef20a8cdfed427d5e651d37907e75"><strong>bref/Bref3.java</strong></a>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +38,7 @@ import vcf.Samples;</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC38" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="old_line diff-line-num" 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">
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Bref3</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="40" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="41" 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="LC41" 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="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">program</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"bref3.<span class="idiff left right">28Jun21.220</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="41" 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="LC41" 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="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">program</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"bref3.<span class="idiff left right">08Feb22.fa4</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
</pre>
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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>
</pre>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The {@code main()} method is the entry point to the bref program.</span></span>
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<br>
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<li id="dcb0e12a67291331c7d1fd8dd651714b291527c8">
<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#dcb0e12a67291331c7d1fd8dd651714b291527c8"><strong>bref/UnBref3.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" 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="37" 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">@@ -37,7 +37,7 @@ import vcf.VcfWriter;</td>
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<pre style="margin: 0;"> <span id="LC37" 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="LC38" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">UnBref3</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="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="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">program</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"unbref3.<span class="idiff left right">28Jun21.220</span>.jar"</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;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">program</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"unbref3.<span class="idiff left right">08Feb22.fa4</span>.jar"</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>
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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;"> * The {@code main()} method is the entry point to the bref program.</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">beagle (220208-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 17 Feb 2022 17:19:57 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">beagle (5.2-210628-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Fix d/watch file</span>
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<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Dylan Aïssi <daissi@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> javahelper</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends-Indep: default-jdk,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libhtsjdk-java</span>
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<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#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">@@ -68,17 +68,17 @@ public class Main {</td>
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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="cm" style="color: #998; font-style: italic;"> * The program name and version.</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;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"(version 5.<span class="idiff left right">2</span>)"</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;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"(version 5.<span class="idiff left right">3</span>)"</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>
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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="cm" style="color: #998; font-style: italic;"> * The program name and version.</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The program name and <span class="idiff left right">commit </span>version.</span></span>
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<pre style="margin: 0;"> <span id="LC75" 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="LC76" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.<span class="idiff left right">28Jun21.220</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.<span class="idiff left right">08Feb22.fa4</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The command to invoke the program.</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;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.<span class="idiff left right">28Jun21.220</span>.jar"</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="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.<span class="idiff left right">08Feb22.fa4</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"> <span class="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;"> * 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">@@ -191,8 +191,8 @@ public class Main {</td>
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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;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">it</span><span class="o" style="font-weight: 600;">()<</span><span class="n" style="color: #333;">nIts</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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192
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">t0</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nanoTime</span><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 class="nc" style="color: #458; font-weight: 600;">PhaseLS</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">runStage1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC194" 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;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">it</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">burnin</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="LC195" class="line" lang="java"> <span class="n" style="color: #333;">runStats</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printEstimated<span class="idiff left">Ne</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pd</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">ne</span></span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC194" 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;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">it</span><span class="o" style="font-weight: 600;">()==</span><span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">burnin</span><span class="o" style="font-weight: 600;">()</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">par</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">em</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">()</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="java"> <span class="n" style="color: #333;">runStats</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printEstimated<span class="idiff left">Parameters</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pd</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">ne</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pd</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">pMismatch</span></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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="java"> <span class="n" style="color: #333;">runStats</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">printStage1Info</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">it</span><span class="o" style="font-weight: 600;">(),</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">System</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">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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<pre style="margin: 0;"> <span id="LC198" class="line" lang="java"> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">incrementIt</span><span class="o" style="font-weight: 600;">();</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#eb9d1a1acbc4ec0ffa4eeee52a6d83ce5c15c2e1"><strong>main/Par.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">@@ -35,6 +35,7 @@ import java.util.Map;</td>
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<pre style="margin: 0;"> <span id="LC35" 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;">Par</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>
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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="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">args</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="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">noNThreads</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="c1" style="color: #998; font-style: italic;">// data parameters</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">File</span> <span class="n" style="color: #333;">gt</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,6 +65,7 @@ public final class Par {</td>
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<pre style="margin: 0;"> <span id="LC65" 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;">gp</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// general parameters</span></span>
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<pre style="margin: 0;">+<span id="LC68" 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;">em</span><span class="o" style="font-weight: 600;">;</span></span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">ne</span><span class="o" style="font-weight: 600;">;</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">;</span></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">window</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">@@ -93,7 +95,8 @@ public final class Par {</td>
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93
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="no" style="color: #008080;">D_GP</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>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="java"></span>
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95
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// default general parameters</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">D_NE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1_000_000</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="no" style="color: #008080;">D_EM</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">D_NE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100_000</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">D_ERR</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MIN_VALUE</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">D_WINDOW</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">40.0f</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="no" style="color: #008080;">D_OVERLAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0f</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="150" 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="153" 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">@@ -150,17 +153,20 @@ public final class Par {</td>
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150
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="java"> <span class="n" style="color: #333;">imp_step</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">floatArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"imp-step"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_IMP_STEP</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">FMIN</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">FMAX</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="n" style="color: #333;">imp_nsteps</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"imp-nsteps"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_IMP_NSTEPS</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="no" style="color: #008080;">IMAX</span><span class="o" style="font-weight: 600;">);</span></span>
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152
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="java"> <span class="n" style="color: #333;">cluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">floatArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"cluster"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_CLUSTER</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 class="no" style="color: #008080;">FMAX</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;">ap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">booleanArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ap"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;"><span class="idiff left">D_AP</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">false</span></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="n" style="color: #333;">gp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">booleanArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"gp"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;"><span class="idiff left">D_GP</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kc" style="font-weight: 600;"><span class="idiff right">false</span></span><span class="o" style="font-weight: 600;">);</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="java"> <span class="n" style="color: #333;">ap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">booleanArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ap"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;"><span class="idiff left">false</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff right">D_AP</span></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;">gp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">booleanArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"gp"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</span><span class="o" style="font-weight: 600;">,</span> <span class="kc" style="font-weight: 600;"><span class="idiff left">false</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff right">D_GP</span></span><span class="o" style="font-weight: 600;">);</span></span>
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155
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="java"></span>
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156
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// general parameters</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> <span class="n" style="color: #333;">em</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">booleanArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"em"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_EM</span><span class="o" style="font-weight: 600;">);</span></span>
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157
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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;">ne</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">floatArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ne"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_NE</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">FMIN</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">FMAX</span><span class="o" style="font-weight: 600;">);</span></span>
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158
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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;">err</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">floatArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"err"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_ERR</span><span class="o" style="font-weight: 600;">,</span> <span class="o" style="font-weight: 600;">-</span><span class="no" style="color: #008080;">FMIN</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">FMAX</span><span class="o" style="font-weight: 600;">);</span></span>
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159
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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;">window</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">floatArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"window"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_WINDOW</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">FMIN</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1000</span><span class="o" style="font-weight: 600;">);</span></span>
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160
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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;">overlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">floatArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"overlap"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_OVERLAP</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">FMIN</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">IMAX</span><span class="o" style="font-weight: 600;">);</span></span>
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161
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="java"> <span class="n" style="color: #333;">buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">floatArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"buffer"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_BUFFER</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">FMIN</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">IMAX</span><span class="o" style="font-weight: 600;">);</span></span>
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162
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java"> <span class="n" style="color: #333;">seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">longArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"seed"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_SEED</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">LMIN</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">LMAX</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;">nthreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modNthreads</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"nthreads"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_NTHREADS</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="no" style="color: #008080;">IMAX</span><span class="o" style="font-weight: 600;">));</span></span>
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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;">rawNThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">intArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"nthreads"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="no" style="color: #008080;">D_NTHREADS</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="no" style="color: #008080;">IMAX</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;">noNThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rawNThreads</span><span class="o" style="font-weight: 600;">==</span><span class="no" style="color: #008080;">D_NTHREADS</span><span class="o" style="font-weight: 600;">;</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="java"> <span class="n" style="color: #333;">nthreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">noNThreads</span> <span class="o" style="font-weight: 600;">?</span> <span class="nc" style="color: #458; font-weight: 600;">Runtime</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRuntime</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">availableProcessors</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">rawNThreads</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>
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// undocumented parameters</span></span>
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166
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="java"> <span class="n" style="color: #333;">truth</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getFile</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Validate</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stringArg</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"truth"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argsMap</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="kc" style="font-weight: 600;">null</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -176,6 +182,16 @@ public final class Par {</td>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clone</span><span class="o" style="font-weight: 600;">();</span></span>
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177
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="java"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns {@code true} if the command line does not include an</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * nthreads parameter and returns {@code false otherwise}.</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return {@code true} if the command line does not include an</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * nthreads parameter</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" 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="LC191" 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;">noNThreads</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">noNThreads</span><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 class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="java"></span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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180
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns a description of the Beagle command line arguments.</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return a description of the Beagle command line arguments</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">@@ -209,6 +225,7 @@ public final class Par {</td>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"general parameters ..."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nl</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" ne=<effective population size> (default="</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">D_NE</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;">nl</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" window=<window length in cM> (default="</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">D_WINDOW</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;">nl</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" em=<estimate ne and err parameters (true/false)> (default="</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">D_EM</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;">nl</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 class="s" style="color: #d14;">" overlap=<window overlap in cM> (default="</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">D_OVERLAP</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;">nl</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" seed=<random seed> (default="</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">D_SEED</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;">nl</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" nthreads=<number of threads> (default: machine dependent)"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nl</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">@@ -223,21 +240,6 @@ public final class Par {</td>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ci</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC226" 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="LC227" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the nthreads parameter, which is equal to</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code Runtime.getRuntime().availableProcessors()} if</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code nthreads == Integer.MAX_VALUE}.</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the nthreads parameter</span></span>
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<pre style="margin: 0;">-<span id="LC231" 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="LC232" 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;">modNthreads</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;">nthreads</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;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nthreads</span><span class="o" style="font-weight: 600;">==</span><span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_VALUE</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="nc" style="color: #458; font-weight: 600;">Runtime</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getRuntime</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">availableProcessors</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="java"> <span class="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="LC237" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nthreads</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="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="LC243" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// data parameters</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC245" 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">@@ -430,6 +432,14 @@ public final class Par {</td>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// general parameters</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC435" 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="LC436" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the em parameter.</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the em parameter</span></span>
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<pre style="margin: 0;">+<span id="LC438" 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="LC439" 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;">em</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="LC440" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">em</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC443" 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="LC444" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns the ne parameter</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the ne parameter</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#611062e8e142f9ef1d5f5200bb13b0a16611898e"><strong>main/RunStats.java</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,6 +23,7 @@ import blbutil.FileUtil;</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">blbutil.Utilities</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.io.File</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.io.PrintWriter</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Optional</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">vcf.Data</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">vcf.Marker</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">@@ -62,9 +63,16 @@ public class RunStats {</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * file and to standard output.</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;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printStartInfo</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="LC66" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">argList</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">noNThreads</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="c1" style="color: #998; font-style: italic;">// add nthreads parameter to list of command line parameters</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">oldLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="java"> <span class="n" style="color: #333;">argList</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">copyOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">argList</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">argList</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="java"> <span class="n" style="color: #333;">argList</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">oldLength</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"nthreads="</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nthreads</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">duoPrint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SHORT_HELP</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">duoPrintln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Start time: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">timeStamp</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">duoPrint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">commandLine</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">PROGRAM</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left">par</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">args</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="LC75" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">duoPrint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">commandLine</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">PROGRAM</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;"><span class="idiff left right">argList</span></span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ped</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 class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"WARNING: This version will not model"</span></span>
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" duos or trios in the pedigree file"</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">@@ -253,15 +261,14 @@ public class RunStats {</td>
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261
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<pre style="margin: 0;"> <span id="LC261" 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="LC262" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Prints the specified estimated effective population size.</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param ne the estimated effective population size</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @<span class="idiff left right">throws IllegalArgumentException if {@code ne < 1}</span></span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @<span class="idiff left right">param pMismatch the estimated allele mismatch parameter</span></span></span>
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<pre style="margin: 0;"> <span id="LC265" 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="LC258" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printEstimatedNe</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ne</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ne</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="LC260" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ne</span><span class="o" style="font-weight: 600;">));</span></span>
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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="LC266" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printEstimatedParameters</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ne</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">pMismatch</span><span class="o" style="font-weight: 600;">)</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="LC267" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">duoPrintln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">log</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>
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">duoPrint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"%1$-31s"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Estimated ne:"</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">duoPrintln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ne</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">duoPrint</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"%1$-31s"</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"Estimated err:"</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">duoPrintln</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">format</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"%1$7.1e"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pMismatch</span><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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#4321c8a41eba5c2d331cb0edb16f56f6fb705039"><strong>phase/HmmParamData.java</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,9 +46,6 @@ public class HmmParamData {</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[][]</span> <span class="n" style="color: #333;">savedBwd</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">emProbs</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="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="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">isHom</span><span class="o" style="font-weight: 600;">;</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">maxErrMaf</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">FloatArray</span> <span class="n" style="color: #333;">markerToMaf</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mismatchCnt</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumMismatchProb</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumGenDist</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">@@ -58,18 +55,9 @@ public class HmmParamData {</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Creates a {@code HmmParamData} instance for the specified data.</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;"> *</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;"> * @param phaseIbs the IBS haplotype segments</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 maxErrMaf the maximum minor allele frequency for which allele</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;"> * allele mismatch probabilities will be estimated</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 IllegalArgumentException 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 maxErrMaf <= 0.0 || maxErrMaf >= 1.0</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;"> * || Float.isFinite(maxErrMaf) == false}</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;"> * @throws NullPointerException if {@code phaseIbs == null}</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="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">HmmParamData</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">maxErrMaf</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="LC69" 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;">maxErrMaf</span><span class="o" style="font-weight: 600;"><=</span><span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">maxErrMaf</span><span class="o" style="font-weight: 600;">>=</span><span class="mf" style="color: #099;">1.0</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="java"> <span class="o" style="font-weight: 600;">||</span> <span class="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFinite</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">maxErrMaf</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="LC71" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">maxErrMaf</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nf" style="color: #900; font-weight: 600;">HmmParamData</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</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="LC61" 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;">phaseData</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">phaseData</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="nc" style="color: #458; font-weight: 600;">FixedPhaseData</span> <span class="n" style="color: #333;">fpd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fpd</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">gt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stage1TargGT</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">@@ -86,9 +74,6 @@ public class HmmParamData {</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">pMismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pMismatch</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;">emProbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">[]</span> <span class="o" style="font-weight: 600;">{</span><span class="mi" style="color: #099;">1</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pMismatch</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pMismatch</span><span class="o" style="font-weight: 600;">};</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC89" 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;">isHom</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</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="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;">markerToMaf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stage1Maf</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: #008080;">maxErrMaf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxErrMaf</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mismatchCnt</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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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;">sumMismatchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</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;">sumGenDist</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</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">@@ -113,6 +98,10 @@ public class HmmParamData {</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addEstimationData</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</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="LC99" class="line" lang="java"> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addMismatchData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mismatchCnt</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sumMismatchProb</span><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 class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addSwitchData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sumGenDist</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sumSwitchProb</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="java"> <span class="n" style="color: #333;">mismatchCnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="java"> <span class="n" style="color: #333;">sumMismatchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</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="n" style="color: #333;">sumGenDist</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</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="n" style="color: #333;">sumSwitchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC107" 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">@@ -135,7 +124,6 @@ public class HmmParamData {</td>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code sample < 0 || sample >= this.nTargSamples()}</span></span>
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<pre style="margin: 0;"> <span id="LC125" 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="LC126" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">update</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="LC138" class="line" lang="java"> <span class="n" style="color: #333;">setIsHom</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="LC127" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nStates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">states</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ibsStates</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">alMatch</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span> <span class="c1" style="color: #998; font-style: italic;">// otherwise hFactor = nStates/(nStates - 1) is NaN</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="java"> <span class="n" style="color: #333;">getParamData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">alMatch</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">],</span> <span class="n" style="color: #333;">nStates</span><span class="o" style="font-weight: 600;">);</span></span>
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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">@@ -183,10 +171,8 @@ public class HmmParamData {</td>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="java"> <span class="n" style="color: #333;">mismatchSum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">stateProb</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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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;">isHom</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;">markerToMaf</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;">m</span><span class="o" style="font-weight: 600;">)<=</span><span class="n" style="color: #333;">maxErrMaf</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="LC187" class="line" lang="java"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">mismatchCnt</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="java"> <span class="n" style="color: #333;">sumMismatchProb</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mismatchSum</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">stateSum</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC189" 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 class="n" style="color: #333;">mismatchCnt</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="java"> <span class="n" style="color: #333;">sumMismatchProb</span> <span class="o" style="font-weight: 600;">+=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">mismatchSum</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">stateSum</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="LC176" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">switchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hFactor</span><span class="o" style="font-weight: 600;">*(</span><span class="mf" style="color: #099;">1.0f</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">jointStateSum</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">stateSum</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">switchProb</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">0.0</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="LC178" class="line" lang="java"> <span class="n" style="color: #333;">sumGenDist</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">genDist</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;">m</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">@@ -194,12 +180,4 @@ public class HmmParamData {</td>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<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;">fwdSum</span><span class="o" style="font-weight: 600;">;</span></span>
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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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<pre style="margin: 0;">-<span id="LC197" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC198" 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;">setIsHom</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="LC199" 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;">isHom</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;">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="LC200" 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;">gt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele1</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC201" 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;">gt</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">allele2</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">sample</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="java"> <span class="n" style="color: #333;">isHom</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="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;">a2</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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<pre style="margin: 0;">-<span id="LC204" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC183" 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/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#4af4ff2035566714b46668721223bba4a04beaf0"><strong>phase/ParamEstimates.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">@@ -44,60 +44,55 @@ public class ParamEstimates {</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</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;"> * Records the specified allele mismatch data if {@code markerCnt > 0}</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;"> * Records the specified allele mismatch data if {@code markerCnt} and</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;"> * {@code pMismatchSum} are finite positive values.</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 markerCnt the number of markers with mismatch data</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 pMismatchSum the sum of estimated allele mismatch probabilities</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;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addMismatchData</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;">markerCnt</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pMismatchSum</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;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markerCnt</span><span class="o" style="font-weight: 600;">></span><span class="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="LC53" 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;">markerCnt</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</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">pMismatchSum</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="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Double</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">isFinite</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pMismatchSum</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="java"> <span class="n" style="color: #333;">mismatchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">MismatchData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">markerCnt</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">pMismatchSum</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 class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="java"></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;">/**</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;"> * Records the specified genetic distance and switch probability</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;"> * if {@code genDistances > 0}.</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;"> * if {@code genDistances} and {@code switchProbs} are finite positive</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;"> * values.</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 genDistances the list of genetic distance</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param switchProbs the list of haplotype switch probabilities</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;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">addSwitchData</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">genDistances</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">switchProbs</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="LC64" 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;">genDistances</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="LC66" 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;">genDistances</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;">switchProbs</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="java"> <span class="o" style="font-weight: 600;">&&</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFinite</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genDistances</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFinite</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">switchProbs</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="n" style="color: #333;">switchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">RecombData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">genDistances</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">switchProbs</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 class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"></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;">/**</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;"> * Returns the estimated allele mismatch rate. <span class="idiff left"> </span>Returns <span class="idiff right">0 if there is</span></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;"> * no data to estimate the allele mismatch rate. The returned<span class="idiff left right"> value is not</span></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;"> * an atomic snapshot. Invocation in the absence of concurrent</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;"> * Returns the estimated allele mismatch rate. Returns <span class="idiff left right">{@code Float.NaN}</span></span></span>
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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 class="idiff left right">if there is </span>no data to estimate the allele mismatch rate. The returned</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">value is not </span>an atomic snapshot. Invocation in the absence of concurrent</span></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;"> * update will return an accurate result, but concurrent updates that</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;"> * occur white the sum is being calculated might not be incorporated</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;"> * in the returned result.</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;"> * @return the estimated allele mismatch rate</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;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC81" 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;">pMismatch</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="LC79" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MismatchData</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mda</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mismatchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">MismatchData</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sumMarkers</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumPMismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</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="nc" style="color: #458; font-weight: 600;">MismatchData</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">mda</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mismatchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stream</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sorted</span><span class="o" style="font-weight: 600;">()</span> <span class="c1" style="color: #998; font-style: italic;">// ensures sum of values is repeatable</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">MismatchData</span><span class="o" style="font-weight: 600;">[]::</span><span class="k" style="font-weight: 600;">new</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">sumMarkers</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumPMismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">d</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;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">MismatchData</span> <span class="n" style="color: #333;">md</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">mda</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="n" style="color: #333;">sumMarkers</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">md</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">markerCnt</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="n" style="color: #333;">sumPMismatch</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">md</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pMismatchSum</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sumMarkers</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="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="n" style="color: #333;"><span class="idiff right">f</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sumPMismatch</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">sumMarkers</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="n" style="color: #333;">sumMarkers</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">Float</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">NaN</span></span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sumPMismatch</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">sumMarkers</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="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;"> * Clears all data that has been added via the</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;"> * {@code this.addMismatchData} and {@code this.addSwitchData()}</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;"> * methods.</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;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">clear</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="LC95" class="line" lang="java"> <span class="n" style="color: #333;">switchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="java"> <span class="n" style="color: #333;">mismatchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> <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>
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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="cm" style="color: #998; font-style: italic;"> * Returns the estimated recombination intensities. Returns {@code 0f}</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;"> * Returns the estimated recombination intensities. Returns {@code Float.NaN}</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;"> * if there is no data from which to estimate recombination intensities.</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;"> * The returned value is NOT an atomic snapshot. An accurate result is</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;"> * guaranteed only if no concurrent updates occur during method</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">@@ -105,17 +100,29 @@ public class ParamEstimates {</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the estimated recombination intensities</span></span>
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<pre style="margin: 0;"> <span id="LC101" 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="LC102" 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;">recombIntensity</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">RecombData</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">rda</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">switchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">RecombData</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumSwitches</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumDistances</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">RecombData</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">rda</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">switchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stream</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sorted</span><span class="o" style="font-weight: 600;">()</span> <span class="c1" style="color: #998; font-style: italic;">// ensures sum of values is repeatable</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RecombData</span><span class="o" style="font-weight: 600;">[]::</span><span class="k" style="font-weight: 600;">new</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumSwitches</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumDistances</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">d</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;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RecombData</span> <span class="n" style="color: #333;">rd</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">rda</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="LC109" class="line" lang="java"> <span class="n" style="color: #333;">sumSwitches</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">switchProb</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="java"> <span class="n" style="color: #333;">sumDistances</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">genDistance</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sumDistances</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sumSwitches</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">sumDistances</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sumDistances</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">?</span> <span class="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">NaN</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sumSwitches</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">sumDistances</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC115" 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="LC116" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Clears all data that has been added via the</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * {@code this.addMismatchData} and {@code this.addSwitchData()}</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * methods.</span></span>
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<pre style="margin: 0;">+<span id="LC119" 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="LC120" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">clear</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="LC121" class="line" lang="java"> <span class="n" style="color: #333;">switchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="java"> <span class="n" style="color: #333;">mismatchData</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="java"> <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>
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<pre style="margin: 0;">-<span id="LC118" 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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RecombData</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="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RecombData</span> <span class="kd" style="font-weight: 600;"><span class="idiff left">implements</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Comparable</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">RecombData</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="LC126" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">genDistance</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">switchProb</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">@@ -124,9 +131,15 @@ public class ParamEstimates {</td>
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<pre style="margin: 0;"> <span id="LC131" 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;">genDistance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genDistance</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">switchProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">switchProb</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="java"> <span class="nd">@Override</span></span>
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<pre style="margin: 0;">+<span id="LC136" 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;">compareTo</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RecombData</span> <span class="n" style="color: #333;">o</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="LC137" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compare</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">genDistance</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">genDistance</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">val</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;">val</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compare</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">switchProb</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">switchProb</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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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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<pre style="margin: 0;">-<span id="LC129" 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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MismatchData</span> <span class="o" style="font-weight: 600;">{</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MismatchData</span> <span class="kd" style="font-weight: 600;"><span class="idiff left">implements</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Comparable</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">MismatchData</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="LC143" class="line" lang="java"></span>
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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;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">markerCnt</span><span class="o" style="font-weight: 600;">;</span></span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pMismatchSum</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">@@ -135,5 +148,11 @@ public class ParamEstimates {</td>
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">markerCnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markerCnt</span><span class="o" style="font-weight: 600;">;</span></span>
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149
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<pre style="margin: 0;"> <span id="LC149" 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;">pMismatchSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pMismatchSum</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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151
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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="nd">@Override</span></span>
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<pre style="margin: 0;">+<span id="LC153" 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;">compareTo</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">MismatchData</span> <span class="n" style="color: #333;">o</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Double</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compare</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pMismatchSum</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pMismatchSum</span><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;">val</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;">val</span> <span class="o" style="font-weight: 600;">:</span> <span class="nc" style="color: #458; font-weight: 600;">Integer</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">compare</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">markerCnt</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">markerCnt</span><span class="o" style="font-weight: 600;">);</span></span>
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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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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="java"> <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></pre>
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<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#feb7a9a924cfaa0b13e7c2647499887d74f2b2bb"><strong>phase/PhaseData.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">@@ -109,7 +109,7 @@ public class PhaseData {</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @return the effective population size</span></span>
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<pre style="margin: 0;"> <span id="LC110" 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="LC111" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">ne</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">recombIntensity</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="LC112" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left right">floor</span></span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">25</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">recombIntensity</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="na" style="color: #008080;">fpd</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nHaps</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;"><span class="idiff left right">ceil</span></span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">25</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">recombIntensity</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="na" style="color: #008080;">fpd</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nHaps</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="java"> <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>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/-/compare/cafc0a68ee2b99103a9b134e50eca15efe1e90b1...a8e5fbe0c92e879bb47772d921f94a1072423b5c#d0875a14cecab64969d49fa0ec30b89961d311ed"><strong>phase/PhaseLS.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">@@ -18,7 +18,6 @@</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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="java"><span class="kn" style="font-weight: 600;">package</span> <span class="nn" style="color: #555;">phase</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.FloatArray</span><span class="o" style="font-weight: 600;">;</span></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.MultiThreadUtils</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;">blbutil.Utilities</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 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,8 +37,6 @@ import vcf.GT;</td>
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<pre style="margin: 0;"> <span id="LC37" 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="LC38" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PhaseLS</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="LC41" 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="nc" style="color: #458; font-weight: 600;">Float</span> <span class="no" style="color: #008080;">MIN_PMISMATCH</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">12</span><span class="n" style="color: #333;">f</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="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="nf" style="color: #900; font-weight: 600;">PhaseLS</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="LC41" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// private constructor to prevent instantiation</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,16 +48,19 @@ public class PhaseLS {</td>
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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="kd" style="font-weight: 600;">public</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;">runStage1</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</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="LC50" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Par</span> <span class="n" style="color: #333;">par</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fpd</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">par</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">it</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nthreads</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="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;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fpd</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">targGT</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nSamples</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nBurninIts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">burnin</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="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pbwtPhaseIbs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</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;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">it</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="LC59" class="line" lang="java"> <span class="n" style="color: #333;">initializeParameters</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">it</span><span class="o" style="font-weight: 600;">()<</span><span class="n" style="color: #333;">nBurninIts</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="LC62" class="line" lang="java"> <span class="n" style="color: #333;">resetPMismatchToDefault</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">);</span> <span class="c1" style="color: #998; font-style: italic;">// only update pMismatch once</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="java"> <span class="n" style="color: #333;">updateParameters</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</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;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">em</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="LC57" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">seed</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC58" 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;">it</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="LC59" class="line" lang="java"> <span class="n" style="color: #333;">initializeParameters</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="java"> <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="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nBurninIts</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="LC62" class="line" lang="java"> <span class="n" style="color: #333;">updateParameters</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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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 class="nc" style="color: #458; font-weight: 600;">AtomicInteger</span> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicInteger</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ExecutorService</span> <span class="n" style="color: #333;">es</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Executors</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">newFixedThreadPool</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nThreads</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">@@ -87,100 +87,40 @@ public class PhaseLS {</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">phaseIbs</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">initializeParameters</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</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="LC90" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">initializeParameters</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">Random</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">rand</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">phaseData</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="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">seed</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</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="n" style="color: #333;">getParamEst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC95" 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;">isBigDecrease</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</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="n" style="color: #333;">decreaseRecombIntensity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="java"> <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;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isBigIncrease</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</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="LC99" class="line" lang="java"> <span class="n" style="color: #333;">increaseRecombIntensity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nTries</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">recombIntensity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</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;">boolean</span> <span class="n" style="color: #333;">finished</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recombIntensity</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</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;">while</span> <span class="o" style="font-weight: 600;">(++</span><span class="n" style="color: #333;">nTries</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">6</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">finished</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="LC105" class="line" lang="java"> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateRecombIntensity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</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="n" style="color: #333;">getParamEst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="java"> <span class="n" style="color: #333;">recombIntensity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recombIntensity</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">)</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="n" style="color: #333;">finished</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="o" style="font-weight: 600;">;</span></span>
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110
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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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111
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<pre style="margin: 0;">-<span id="LC111" 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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112
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<td class="new_line diff-line-num old" data-linenumber="92" 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="LC112" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">dec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">()<</span><span class="mf" style="color: #099;">0.9f</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="old_line diff-line-num old" 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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<td class="new_line diff-line-num old" data-linenumber="92" 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="LC113" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">inc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">()></span><span class="mf" style="color: #099;">1.1111f</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</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="n" style="color: #333;">finished</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dec</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;">inc</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>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">prevRecInt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">();</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxInitialIts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span><span class="o" style="font-weight: 600;">;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" 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;">maxInitialIts</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="LC95" class="line" lang="java"> <span class="n" style="color: #333;">updateParameters</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">recInt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">abs</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recInt</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">prevRecInt</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">0.1</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prevRecInt</span><span class="o" style="font-weight: 600;">)</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="k" style="font-weight: 600;">break</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 class="n" style="color: #333;">prevRecInt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">recInt</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="java"> <span class="n" style="color: #333;">updateParams</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">);</span></span>
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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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<pre style="margin: 0;"> <span id="LC103" class="line" lang="java"></span>
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120
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<pre style="margin: 0;">-<span id="LC120" 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;">updateParameters</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</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="LC104" 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;">updateParameters</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">)</span> <span class="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="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getParamEst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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121
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">phaseData</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 class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">phaseData</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">seed</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</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="n" style="color: #333;">getParamEst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="java"> <span class="n" style="color: #333;">updateParams</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC128" 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;">updateParams</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">prevPMismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pMismatch</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="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">pMismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pMismatch</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">recombIntensity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">pMismatch</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="n" style="color: #333;"><span class="idiff right">f</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="java"> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updatePMismatch</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">Math</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">max</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pMismatch</span></span><span class="o" style="font-weight: 600;"><span class="idiff">,</span></span><span class="idiff"> </span><span class="no" style="color: #008080;"><span class="idiff">MIN_PMISMATCH</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="LC110" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">Float</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">isFinite</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pMismatch</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pMismatch</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="n" style="color: #333;"><span class="idiff right">prevPMismatch</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="java"> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updatePMismatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left right">pMismatch</span></span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recombIntensity</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</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="LC113" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">Float</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">isFinite</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">recombIntensity</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">recombIntensity</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</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="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateRecombIntensity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">recombIntensity</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 class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="java"></span>
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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;">void</span> <span class="nf" style="color: #900; font-weight: 600;">decreaseRecombIntensity</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">phaseData</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="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isBigDecrease</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</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="LC143" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">nextRI</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="mf" style="color: #099;">0.333f</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">(),</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateRecombIntensity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nextRI</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="n" style="color: #333;">getParamEst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">increaseRecombIntensity</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</span><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 class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">phaseData</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="k" style="font-weight: 600;">while</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">isBigIncrease</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</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="LC154" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">nextRI</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">3</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><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="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="java"> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updateRecombIntensity</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nextRI</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="java"> <span class="n" style="color: #333;">getParamEst</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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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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<pre style="margin: 0;">-<span id="LC159" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC161" 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;">isBigDecrease</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</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="LC162" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">estRI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">estRI</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">estRI</span><span class="o" style="font-weight: 600;"><</span><span class="mf" style="color: #099;">0.8f</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC166" 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;">isBigIncrease</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</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="LC167" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">estRI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">estRI</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;">estRI</span><span class="o" style="font-weight: 600;">></span><span class="mf" style="color: #099;">1.25f</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">recombIntensity</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC171" 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;">resetPMismatchToDefault</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</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="LC172" class="line" lang="java"> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">updatePMismatch</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Par</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">liStephensPMismatch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fpd</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nHaps</span><span class="o" style="font-weight: 600;">()));</span></span>
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<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>
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<pre style="margin: 0;">-<span id="LC175" 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;">getParamEst</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="java"> <span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">clear</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="nf" style="color: #900; font-weight: 600;">getParamEst</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PbwtPhaseIbs</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</span> <span class="n" style="color: #333;">paramEst</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">ParamEstimates</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="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">phaseData</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">FixedPhaseData</span> <span class="n" style="color: #333;">fpd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">fpd</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sampleIndices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samplesToAnalyze</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nThreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">par</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nthreads</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">sampleIndices</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">mafPercentile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.05f</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">maxErrMaf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxMismatchMaf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">fpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">stage1Maf</span><span class="o" style="font-weight: 600;">(),</span> <span class="n" style="color: #333;">mafPercentile</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="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">20000.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nThreads</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minIndices</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">AtomicInteger</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">AtomicInteger</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -188,14 +128,14 @@ public class PhaseLS {</td>
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<pre style="margin: 0;"> <span id="LC128" 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;">nThreads</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="LC129" class="line" lang="java"> <span class="n" style="color: #333;">es</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">submit</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>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">HmmParamData</span> <span class="n" style="color: #333;">hpd</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HmmParamData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">maxErrMaf</span></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="nc" style="color: #458; font-weight: 600;">HmmParamData</span> <span class="n" style="color: #333;">hpd</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">HmmParamData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">phaseIbs</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAndIncrement</span><span class="o" style="font-weight: 600;">();</span></span>
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133
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<pre style="margin: 0;"> <span id="LC133" 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;">hpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sumSwitchProbs</span><span class="o" style="font-weight: 600;">()<</span><span class="n" style="color: #333;">maxSum</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;">minIndices</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 class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">sampleIndices</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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195
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="java"> <span class="n" style="color: #333;">hpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">update</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sampleIndices</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="java"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counter</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAndIncrement</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="n" style="color: #333;">hpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addEstimationData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">paramEst</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC138" 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 class="n" style="color: #333;">hpd</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">addEstimationData</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">paramEst</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="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;">catch</span> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Throwable</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">)</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="nc" style="color: #458; font-weight: 600;">Utilities</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">exit</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -203,6 +143,7 @@ public class PhaseLS {</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="java"> <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="LC144" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">MultiThreadUtils</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">shutdownExecService</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">es</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">paramEst</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="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">samplesToAnalyze</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">PhaseData</span> <span class="n" style="color: #333;">pd</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="n" style="color: #333;">rand</span><span class="o" style="font-weight: 600;">)</span> <span class="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">@@ -220,23 +161,6 @@ public class PhaseLS {</td>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC223" 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;">float</span> <span class="nf" style="color: #900; font-weight: 600;">maxMismatchMaf</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">FloatArray</span> <span class="n" style="color: #333;">maf</span><span class="o" style="font-weight: 600;">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">perc</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="LC224" 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;">perc</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #099;">0</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">perc</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">1</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">||</span> <span class="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isFinite</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">perc</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="LC225" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">perc</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">sortedMaf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">IntStream</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">range</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">maf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">())</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">parallel</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">mapToDouble</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;">maf</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>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sorted</span><span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="java"> <span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toArray</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">-<span id="LC232" 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="nc" style="color: #458; font-weight: 600;">Arrays</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">binarySearch</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sortedMaf</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MIN_VALUE</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;">if</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;">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="LC234" class="line" lang="java"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="java"> <span class="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="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">)</span> <span class="nc" style="color: #458; font-weight: 600;">Math</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">floor</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">perc</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">sortedMaf</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">)</span> <span class="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;">sortedMaf</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="nc" style="color: #458; font-weight: 600;">Float</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MIN_VALUE</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sortedMaf</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">]);</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="java"> <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>
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<pre style="margin: 0;"> <span id="LC164" 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="LC165" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Returns phased genotypes at all markers.</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * @param pd estimated phased genotypes at stage 1 markers</span></span>
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