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<h3>
Dylan Aïssi pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/beagle">Debian Med / beagle</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/516930171ac0954afead01ef7c14db5c310caf0b">51693017</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2019-11-21T06:06:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.1-191120+dfsg</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
</a>
</li>
<li class="file-stats">
<a href="#ec6a94af868b7dfb86724b44ca474651fa26375a">
vcf/RefIt.java
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="2ad0efaccf66628e1858a4c133e8914e33eb2221">
<a href="https://salsa.debian.org/med-team/beagle/commit/516930171ac0954afead01ef7c14db5c310caf0b#2ad0efaccf66628e1858a4c133e8914e33eb2221"><strong>main/Main.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,8 +65,8 @@ public class Main {</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The program name and version.</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"(version 5.1)"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.<span class="idiff left right">08Nov19.3ec</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.<span class="idiff left right">08Nov19.3ec</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.<span class="idiff left right">20Nov19.573</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.<span class="idiff left right">20Nov19.573</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The copyright string.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -78,7 +78,7 @@ public class Main {</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">SHORT_HELP</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">VERSION</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">COPYRIGHT</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Enter \"java -jar beagle.<span class="idiff left right">08Nov19.3ec</span>.jar\" to "</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Enter \"java -jar beagle.<span class="idiff left right">20Nov19.573</span>.jar\" to "</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"list command line argument"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Par</span> <span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">;</span></span>
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<a href="https://salsa.debian.org/med-team/beagle/commit/516930171ac0954afead01ef7c14db5c310caf0b#ec6a94af868b7dfb86724b44ca474651fa26375a"><strong>vcf/RefIt.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">@@ -69,6 +69,8 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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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="nc" style="color: #458; font-weight: 600;">List</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">midBuffer</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="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;">Deque</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">recBuffer</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;">final</span> <span class="nc" style="color: #458; font-weight: 600;">SeqCoder3</span> <span class="n" style="color: #333;">seqCoder</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="java"> <span class="kd" style="font-weight: 600;">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;">maxSeqCodedAlleles</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="java"> <span class="kd" style="font-weight: 600;">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;">maxSeqCodingMajorCnt</span><span class="o" style="font-weight: 600;">;</span></span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC75" 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;">ExecutorService</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="LC76" class="line" lang="java"></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">@@ -141,6 +143,8 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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141
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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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">markerFilter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">markerFilter</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">seqCoder</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;">SeqCoder3</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">vcfHeader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samples</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC146" 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;">maxSeqCodedAlleles</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;">seqCoder</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">maxNSeq</span><span class="o" style="font-weight: 600;">(),</span> <span class="nc" style="color: #458; font-weight: 600;">SeqCoder3</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">MAX_NALLELES</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">maxSeqCodingMajorCnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxSeqCodingMajorCnt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">vcfHeader</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samples</span><span class="o" style="font-weight: 600;">());</span></span>
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144
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"></span>
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145
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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;">lastChrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span></span>
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146
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<pre style="margin: 0;"> <span id="LC150" 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;">stringBuffer</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;">ArrayBlockingQueue</span><span class="o" style="font-weight: 600;"><>(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -152,6 +156,11 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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152
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="java"> <span class="n" style="color: #333;">fillEmissionBuffer</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="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>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">maxSeqCodingMajorCnt</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">Samples</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nSamples</span><span class="o" style="font-weight: 600;">()</span> <span 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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161
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<pre style="margin: 0;">+<span id="LC161" 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;">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;">nHaps</span><span class="o" style="font-weight: 600;">*</span><span class="nc" style="color: #458; font-weight: 600;">SeqCoder3</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">COMPRESS_FREQ_THRESHOLD</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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162
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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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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="java"></span>
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164
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<pre style="margin: 0;"> <span id="LC164" 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;">startFileReadingThread</span><span class="o" style="font-weight: 600;">(</span><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>
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156
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ArrayBlockingQueue</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="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">firstRec</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">FileIt</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="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">,</span></span>
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bufferSize</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -308,9 +317,9 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sb</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">();</span></span>
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309
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">applySeqCoding</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span> <span class="n" style="color: #333;">rec</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="LC320" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="nf" style="color: #900; font-weight: 600;">applySeqCoding</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">RefGTRec</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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312
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">isAlleleCoded</span><span class="o" style="font-weight: 600;">();</span></span>
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313
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<pre style="margin: 0;">-<span id="LC313" 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;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nAlleles</span><span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">></span><span class="idiff left"> </span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">SeqCoder3</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff right">MAX_NALLELES</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">marker</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">nAlleles</span><span class="o" style="font-weight: 600;">()</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">maxSeqCodedAlleles</span></span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nHaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -321,6 +330,6 @@ public class RefIt implements SampleFileIt<RefGTRec> {</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="java"> <span class="n" style="color: #333;">majCnt</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">alleleCount</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;"><span class="idiff left">(</span></span><span class="nc" style="color: #458; font-weight: 600;"><span class="idiff">SeqCoder3</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="na" style="color: #008080;"><span class="idiff">COMPRESS_FREQ_THRESHOLD</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=(</span></span><span class="mf" style="color: #099;"><span class="idiff">1.0f</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">majCnt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">)/</span></span><span class="n" style="color: #333;"><span class="idiff">nHaps</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="LC333" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left">majCnt</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="n" style="color: #333;"><span class="idiff right">maxSeqCodingMajorCnt</span></span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span></pre>
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