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<h3>
Dylan Aïssi pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/chromhmm">Debian Med / chromhmm</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/chromhmm/-/commit/bd1ced357ad13d08457efd9f61d467e43cd69cb6">bd1ced35</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2020-07-15T10:17:40+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.21+dfsg</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#b878cde2a28128a1ce4a4106b42d1e16efb65f66">
edu/mit/compbio/ChromHMM/BrowserOutput.java
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<li class="file-stats">
<a href="#e1a765a5b2b828119bc810319c6fa07e7300eecf">
edu/mit/compbio/ChromHMM/ChromHMM.java
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<li class="file-stats">
<a href="#7e91b8c750d2f1f3056fc7dcbd7d4d639572d170">
edu/mit/compbio/ChromHMM/Preprocessing.java
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<li class="file-stats">
<a href="#4fb31ca7c49b2c49cfd549091ba94777db11f494">
edu/mit/compbio/ChromHMM/StateAnalysis.java
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/chromhmm/-/commit/bd1ced357ad13d08457efd9f61d467e43cd69cb6#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">See http://compbio.mit.edu/ChromHMM/ or http<span class="idiff left right">://www.biolchem.ucla.edu/labs/ernst</span>/ChromHMM/ for more information on ChromHMM.</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">See http://compbio.mit.edu/ChromHMM/ or http<span class="idiff left right">s://ernstlab.biolchem.ucla.edu</span>/ChromHMM/ for more information on ChromHMM.</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">========</span></span></pre>
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<li id="b878cde2a28128a1ce4a4106b42d1e16efb65f66">
<a href="https://salsa.debian.org/med-team/chromhmm/-/commit/bd1ced357ad13d08457efd9f61d467e43cd69cb6#b878cde2a28128a1ce4a4106b42d1e16efb65f66"><strong>edu/mit/compbio/ChromHMM/BrowserOutput.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="385" 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="385" 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">@@ -385,7 +385,7 @@ public class BrowserOutput</td>
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385
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szFullID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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="c1" style="color: #998; font-style: italic;">//this removes ordering type</span></span>
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386
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<pre style="margin: 0;"> <span id="LC386" 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;">bfirst</span><span class="o" style="font-weight: 600;">)</span></span>
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szout</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"track name=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\"<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szFullID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="LC388" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szout</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"track name=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szFullID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="LC389" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" ordered)"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" visibility=1 itemRgb=\"On\""</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">btformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="java"> <span class="n" style="color: #333;">pwzip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</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;">btformat</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="433" 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="433" 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">@@ -433,7 +433,7 @@ public class BrowserOutput</td>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szID</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szFullID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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="c1" style="color: #998; font-style: italic;">//this removes ordering type</span></span>
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<pre style="margin: 0;"> <span id="LC434" 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;">bfirst</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"track name=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\"<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szFullID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="LC436" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"track name=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szFullID</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="LC437" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" ordered)"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" visibility=1 itemRgb=\"On\""</span><span class="o" style="font-weight: 600;">);</span></span>
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438
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="java"> <span class="n" style="color: #333;">bfirst</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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<pre style="margin: 0;"> <span id="LC439" class="line" lang="java"> <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="559" 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="559" 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">@@ -559,7 +559,7 @@ public class BrowserOutput</td>
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559
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559
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<pre style="margin: 0;"> <span id="LC559" 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;">bgzip</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">GZIPOutputStream</span> <span class="n" style="color: #333;">pwzip</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;">GZIPOutputStream</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;">FileOutputStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szoutputfileprefix</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SZBROWSEREXPANDEDEXTENSION</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".bed.gz"</span><span class="o" style="font-weight: 600;">));</span></span>
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562
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szout</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"track name=\"Expanded_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\"<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="LC562" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szout</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"track name=\"Expanded_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="LC563" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" ordered)"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" visibility=2 itemRgb=\"On\""</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">;</span></span>
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">btformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">();</span></span>
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="java"> <span class="n" style="color: #333;">pwzip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</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;">btformat</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="641" 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">@@ -641,7 +641,7 @@ public class BrowserOutput</td>
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641
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</span> <span class="n" style="color: #333;">pw</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;">PrintWriter</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;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szoutputfileprefix</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SZBROWSEREXPANDEDEXTENSION</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".bed"</span><span class="o" style="font-weight: 600;">));</span></span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"track name=\"Expanded_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\"<span class="idiff left right"> </span>"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="LC644" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"track name=\"Expanded_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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="LC645" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" ordered)"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" visibility=2 itemRgb=\"On\""</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbrowserend</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="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="n" style="color: #333;">hmchromMax</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;">szChroms</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="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">()*.</span><span class="mo" style="color: #099;">001</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="LC647" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"browser position "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szChroms</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="s" style="color: #d14;">":1-"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nbrowserend</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">@@ -699,5 +699,308 @@ public class BrowserOutput</td>
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//////////////////////////////////////////////////////////////////////////////////////////////////</span></span>
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<pre style="margin: 0;">+<span id="LC707" 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="LC708" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Makes a single track browser view of the segmentation represented in szsegmentfile</span></span>
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * szcolormapping is a two or three column text file which maps state ID to R,G,B color triples and optionally a state label</span></span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Name of segmentation in the browser file is given by szsegmentationame</span></span>
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * Output is a file named szoutputfileprefix_browserdense.bed of segmentation viewable with one state per row</span></span>
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<pre style="margin: 0;">+<span id="LC712" 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="LC713" 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;">makebrowserexpandedLowMem</span><span class="o" style="font-weight: 600;">()</span> <span class="kd" style="font-weight: 600;">throws</span> <span class="nc" style="color: #458; font-weight: 600;">IOException</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC715" 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;">bgzip</span><span class="o" style="font-weight: 600;">)</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szoutputfileprefix</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SZBROWSEREXPANDEDEXTENSION</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".bed.gz"</span><span class="o" style="font-weight: 600;">);</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szoutputfileprefix</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SZBROWSEREXPANDEDEXTENSION</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".bed"</span><span class="o" style="font-weight: 600;">);</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="java"></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">;</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="java"></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span> <span class="n" style="color: #333;">brsegment</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szsegmentfile</span><span class="o" style="font-weight: 600;">);</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="java"></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//stores set of chromosomes and labels</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">HashSet</span> <span class="n" style="color: #333;">hschroms</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;">HashSet</span><span class="o" style="font-weight: 600;">();</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">HashSet</span> <span class="n" style="color: #333;">hslabels</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;">HashSet</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="java"></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//stores for each chromosome the maximum coordinate</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span> <span class="n" style="color: #333;">hmchromMax</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;">HashMap</span><span class="o" style="font-weight: 600;">();</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="java"></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="java"></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//maps a label without the prefix back to the full label</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span> <span class="n" style="color: #333;">hmlabelToFull</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;">HashMap</span><span class="o" style="font-weight: 600;">();</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="java"></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabelFull</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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740
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<pre style="margin: 0;">+<span id="LC740" 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;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</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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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="java"> <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="java"></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="java"> <span class="n" style="color: #333;">hmlabelToFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabel</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">);</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="java"></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="java"> <span class="n" style="color: #333;">hschroms</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">);</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="java"> <span class="n" style="color: #333;">hslabels</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabel</span><span class="o" style="font-weight: 600;">);</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//ArrayList alRecs = (ArrayList) hmcoords.get(szchrom+"\t"+szLabel);</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//if (alRecs ==null)</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//{</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//creating first entry for chromsome and coordinate</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// alRecs = new ArrayList();</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// hmcoords.put(szchrom+"\t"+szLabel,alRecs);</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//alRecs.add(new BeginEndRec(nbegin,nend));</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="java"></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//potentially updating maximum coordinate for chromosome</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Object</span> <span class="n" style="color: #333;">obj</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;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmchromMax</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;">szchrom</span><span class="o" style="font-weight: 600;">));</span> </span>
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764
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<pre style="margin: 0;">+<span id="LC764" 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;">obj</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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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nval</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;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="java"> </span>
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768
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<pre style="margin: 0;">+<span id="LC768" 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;">nend</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nval</span><span class="o" style="font-weight: 600;">)</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="java"> <span class="n" style="color: #333;">hmchromMax</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</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;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nend</span><span class="o" style="font-weight: 600;">));</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span> </span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="java"> <span class="n" style="color: #333;">hmchromMax</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</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;">valueOf</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nend</span><span class="o" style="font-weight: 600;">));</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="java"> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="java"></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="java"> </span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//gets all the state labels and sorts them</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" 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;">szLabels</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;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">hslabels</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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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Iterator</span> <span class="n" style="color: #333;">itrLabels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hslabels</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nindex</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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785
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<pre style="margin: 0;">+<span id="LC785" 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;">itrLabels</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="java"> <span class="n" style="color: #333;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nindex</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="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">itrLabels</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">();</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="java"> <span class="n" style="color: #333;">nindex</span><span class="o" style="font-weight: 600;">++;</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="java"> <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;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabels</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;">LabelCompare</span><span class="o" style="font-weight: 600;">());</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="java"></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//gets all the chromsomes and sorts them</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" 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;">szChroms</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;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">hschroms</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 new new_line" data-linenumber="794" 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">
794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">Iterator</span> <span class="n" style="color: #333;">itrChroms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hschroms</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">iterator</span><span class="o" style="font-weight: 600;">();</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="java"> <span class="n" style="color: #333;">nindex</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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796
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<pre style="margin: 0;">+<span id="LC796" 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;">itrChroms</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">hasNext</span><span class="o" style="font-weight: 600;">())</span></span>
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="java"> <span class="n" style="color: #333;">szChroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nindex</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="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">itrChroms</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">next</span><span class="o" style="font-weight: 600;">();</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="java"> <span class="n" style="color: #333;">nindex</span><span class="o" style="font-weight: 600;">++;</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="java"> <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;">sort</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szChroms</span><span class="o" style="font-weight: 600;">);</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="java"></span>
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803
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<pre style="margin: 0;">+<span id="LC803" 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;">bgzip</span><span class="o" style="font-weight: 600;">)</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">GZIPOutputStream</span> <span class="n" style="color: #333;">pwzip</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;">GZIPOutputStream</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;">FileOutputStream</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szoutputfileprefix</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SZBROWSEREXPANDEDEXTENSION</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".bed.gz"</span><span class="o" style="font-weight: 600;">));</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szout</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"track name=\"Expanded_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" ordered)"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" visibility=2 itemRgb=\"On\""</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">;</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">btformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">();</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="java"> <span class="n" style="color: #333;">pwzip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</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;">btformat</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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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="java"></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pw.println("track name=\"Expanded_"+szsegmentationname+"\" description=\" "+szsegmentationname+" ("+ChromHMM.convertCharOrderToStringOrder(szLabelFull.charAt(0))</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// +" ordered)"+"\" visibility=2 itemRgb=\"On\"");</span></span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbrowserend</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="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="n" style="color: #333;">hmchromMax</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;">szChroms</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="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">()*.</span><span class="mo" style="color: #099;">001</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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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="java"> <span class="n" style="color: #333;">szout</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"browser position "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szChroms</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="s" style="color: #d14;">":1-"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nbrowserend</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">;</span></span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="java"> <span class="n" style="color: #333;">btformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">();</span></span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="java"> <span class="n" style="color: #333;">pwzip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</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;">btformat</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="LC818" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pwzip.println("browser position "+szChroms[0]+":1-"+nbrowserend);</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="java"></span>
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820
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<pre style="margin: 0;">+<span id="LC820" 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;">nchrom</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;">nchrom</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">szChroms</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;">nchrom</span><span class="o" style="font-weight: 600;">++)</span></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span> <span class="n" style="color: #333;">hmcoords</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;">HashMap</span><span class="o" style="font-weight: 600;">();</span></span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szChroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">];</span></span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="java"></span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//stores the set of interval coordinates for each chromosome and label</span></span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="java"> <span class="n" style="color: #333;">brsegment</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szsegmentfile</span><span class="o" style="font-weight: 600;">);</span></span>
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827
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<pre style="margin: 0;">+<span id="LC827" 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;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</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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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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831
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<pre style="margin: 0;">+<span id="LC831" 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;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrchrom</span><span class="o" style="font-weight: 600;">))</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="java"> <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="java"></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">alRecs</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;">ArrayList</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcoords</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;">szLabel</span><span class="o" style="font-weight: 600;">);</span></span>
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839
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<pre style="margin: 0;">+<span id="LC839" 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;">alRecs</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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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//creating first entry for chromsome and coordinate</span></span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="java"> <span class="n" style="color: #333;">alRecs</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;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="java"> <span class="n" style="color: #333;">hmcoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">alRecs</span><span class="o" style="font-weight: 600;">);</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="java"> <span class="n" style="color: #333;">alRecs</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nbegin</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nend</span><span class="o" style="font-weight: 600;">));</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="java"> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="java"></span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="java"></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//UCSC browser seems to reverse the ordering of browser track files</span></span>
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852
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<pre style="margin: 0;">+<span id="LC852" 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;">nlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabels</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 class="n" style="color: #333;">nlabel</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;">nlabel</span><span class="o" style="font-weight: 600;">--)</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcolor</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;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcolor</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="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</span><span class="o" style="font-weight: 600;">]);</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//omits those segment labels not observed at all on chromosome</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="java"></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">alRecs</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;">ArrayList</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcoords</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;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</span><span class="o" style="font-weight: 600;">]);</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" 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;">alRecs</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="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="java"></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmax</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;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmchromMax</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;">szChroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">])).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="java"></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//this forces browser to display segment until the end of the chromosome</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="java"> <span class="n" style="color: #333;">alRecs</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nmax</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nmax</span><span class="o" style="font-weight: 600;">));</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="java"></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alRecs</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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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmin</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">alRecs</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)).</span><span class="na" style="color: #008080;">nbegin</span><span class="o" style="font-weight: 600;">;</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfinalend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nmax</span><span class="o" style="font-weight: 600;">;</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="java"></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szoutlabel</span><span class="o" style="font-weight: 600;">;</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szsuffix</span><span class="o" style="font-weight: 600;">;</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" 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;">szsuffix</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;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmlabelExtend</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="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmlabelToFull</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;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</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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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="java"> <span class="n" style="color: #333;">szoutlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</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;">szsuffix</span><span class="o" style="font-weight: 600;">;</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="java"> <span class="n" style="color: #333;">szoutlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</span><span class="o" style="font-weight: 600;">];</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="java"></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringBuffer</span> <span class="n" style="color: #333;">sbout</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;">StringBuffer</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="881" 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">
881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="java"> <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrchrom</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</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="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nfinalend</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szoutlabel</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t0\t.\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nmin</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nfinalend</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcolor</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">nsize</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="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pw.print(szChroms[nchrom]+"\t"+0+"\t"+nfinalend+"\t"+szoutlabel+"\t0\t.\t"+nmin+"\t"+nfinalend+"\t"+szcolor+"\t"+(nsize+1)+"\t");</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pw.print(0); //forcing the display to start at the beginning of the chromosome</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="java"> <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" 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;">ni</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;">ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nsize</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BeginEndRec</span> <span class="n" style="color: #333;">theBeginEndRec</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">alRecs</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;">ni</span><span class="o" style="font-weight: 600;">);</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ndiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theBeginEndRec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">theBeginEndRec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nbegin</span><span class="o" style="font-weight: 600;">;</span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="java"> <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="java"> <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ndiff</span><span class="o" style="font-weight: 600;">);</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pw.print(",");</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pw.print(ndiff);</span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="894" 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">
894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="java"> <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="895" 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">
895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="java"> <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="896" 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">
896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pw.print("\t");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="897" 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">
897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pw.print(0);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="898" 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">
898
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<pre style="margin: 0;">+<span id="LC898" 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;">ni</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;">ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nsize</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="899" 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">
899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nloc</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">alRecs</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;">ni</span><span class="o" style="font-weight: 600;">)).</span><span class="na" style="color: #008080;">nbegin</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="901" 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">
901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="java"> <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="902" 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">
902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="java"> <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nloc</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="903" 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">
903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pw.print(",");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="904" 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">
904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//pw.print(nloc);</span></span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="906" 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">
906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="java"> <span class="n" style="color: #333;">sbout</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">append</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\n"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="907" 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">
907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// pw.println();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="908" 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">
908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="java"> <span class="n" style="color: #333;">btformat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sbout</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 class="na" style="color: #008080;">getBytes</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="909" 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">
909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="java"> <span class="n" style="color: #333;">pwzip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">btformat</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;">btformat</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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<td class="diff-line-num new new_line" data-linenumber="910" 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">
910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="911" 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">
911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="912" 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">
912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="java"> <span class="n" style="color: #333;">pwzip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">finish</span><span class="o" style="font-weight: 600;">();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="913" 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">
913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="java"> <span class="n" style="color: #333;">pwzip</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</span> <span class="n" style="color: #333;">pw</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;">PrintWriter</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;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szoutputfileprefix</span><span class="o" style="font-weight: 600;">+</span><span class="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">SZBROWSEREXPANDEDEXTENSION</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".bed"</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="918" 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">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"track name=\"Expanded_"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" description=\""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szsegmentationname</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="nc" style="color: #458; font-weight: 600;">ChromHMM</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">convertCharOrderToStringOrder</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">charAt</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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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" ordered)"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\" visibility=2 itemRgb=\"On\""</span><span class="o" style="font-weight: 600;">);</span></span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbrowserend</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="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="n" style="color: #333;">hmchromMax</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;">szChroms</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="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">()*.</span><span class="mo" style="color: #099;">001</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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921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"browser position "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szChroms</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="s" style="color: #d14;">":1-"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nbrowserend</span><span class="o" style="font-weight: 600;">);</span></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="java"></span>
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923
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<pre style="margin: 0;">+<span id="LC923" 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;">nchrom</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;">nchrom</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">szChroms</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;">nchrom</span><span class="o" style="font-weight: 600;">++)</span></span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcurrchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szChroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">];</span></span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">HashMap</span> <span class="n" style="color: #333;">hmcoords</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;">HashMap</span><span class="o" style="font-weight: 600;">();</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="928" 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">
928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//stores the set of interval coordinates for each chromosome and label</span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="java"> <span class="n" style="color: #333;">brsegment</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szsegmentfile</span><span class="o" style="font-weight: 600;">);</span></span>
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930
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<pre style="margin: 0;">+<span id="LC930" 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;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</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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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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934
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<pre style="margin: 0;">+<span id="LC934" 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;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrchrom</span><span class="o" style="font-weight: 600;">))</span></span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="938" 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">
938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="java"> <span class="n" style="color: #333;">szLabelFull</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="939" 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">
939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szLabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabelFull</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">substring</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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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="941" 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">
941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">alRecs</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;">ArrayList</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcoords</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;">szLabel</span><span class="o" style="font-weight: 600;">);</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" 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;">alRecs</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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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//creating first entry for chromsome and coordinate</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="java"> <span class="n" style="color: #333;">alRecs</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;">ArrayList</span><span class="o" style="font-weight: 600;">();</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="java"> <span class="n" style="color: #333;">hmcoords</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">put</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLabel</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">alRecs</span><span class="o" style="font-weight: 600;">);</span></span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="java"> <span class="n" style="color: #333;">alRecs</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nbegin</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nend</span><span class="o" style="font-weight: 600;">));</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="java"> <span class="n" style="color: #333;">brsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="java"></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//UCSC browser seems to reverse the ordering of browser track files</span></span>
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954
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<pre style="margin: 0;">+<span id="LC954" 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;">nlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabels</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 class="n" style="color: #333;">nlabel</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;">nlabel</span><span class="o" style="font-weight: 600;">--)</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcolor</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;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcolor</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="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</span><span class="o" style="font-weight: 600;">]);</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="java"></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//omits those segment labels not observed at all on chromosome</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">ArrayList</span> <span class="n" style="color: #333;">alRecs</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;">ArrayList</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmcoords</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;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</span><span class="o" style="font-weight: 600;">]);</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" 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;">alRecs</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="k" style="font-weight: 600;">continue</span><span class="o" style="font-weight: 600;">;</span></span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="java"></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmax</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;">Integer</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmchromMax</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;">szChroms</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nchrom</span><span class="o" style="font-weight: 600;">])).</span><span class="na" style="color: #008080;">intValue</span><span class="o" style="font-weight: 600;">();</span></span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="java"></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//this forces browser to display segment until the end of the chromosome</span></span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="java"> <span class="n" style="color: #333;">alRecs</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nmax</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">nmax</span><span class="o" style="font-weight: 600;">));</span></span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="java"></span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alRecs</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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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nmin</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">alRecs</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="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">)).</span><span class="na" style="color: #008080;">nbegin</span><span class="o" style="font-weight: 600;">;</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfinalend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nmax</span><span class="o" style="font-weight: 600;">;</span></span>
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970
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szoutlabel</span><span class="o" style="font-weight: 600;">;</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szsuffix</span><span class="o" style="font-weight: 600;">;</span></span>
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973
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<pre style="margin: 0;">+<span id="LC973" 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;">szsuffix</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;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmlabelExtend</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="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmlabelToFull</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;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</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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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="java"> <span class="n" style="color: #333;">szoutlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</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;">szsuffix</span><span class="o" style="font-weight: 600;">;</span></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="978" 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">
978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="java"> <span class="n" style="color: #333;">szoutlabel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">szLabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nlabel</span><span class="o" style="font-weight: 600;">];</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="982" 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">
982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcurrchrom</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</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="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nfinalend</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szoutlabel</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t0\t.\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nmin</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nfinalend</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szcolor</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">nsize</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="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="983" 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">
983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</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="c1" style="color: #998; font-style: italic;">//forcing the display to start at the beginning of the chromosome</span></span>
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<td class="diff-line-num new new_line" data-linenumber="984" 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">
984
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<pre style="margin: 0;">+<span id="LC984" 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;">ni</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;">ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nsize</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BeginEndRec</span> <span class="n" style="color: #333;">theBeginEndRec</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">alRecs</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;">ni</span><span class="o" style="font-weight: 600;">);</span></span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ndiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theBeginEndRec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">theBeginEndRec</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nbegin</span><span class="o" style="font-weight: 600;">;</span></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</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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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ndiff</span><span class="o" style="font-weight: 600;">);</span></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</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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993
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<pre style="margin: 0;">+<span id="LC993" 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;">ni</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;">ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nsize</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nloc</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;">BeginEndRec</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">alRecs</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;">ni</span><span class="o" style="font-weight: 600;">)).</span><span class="na" style="color: #008080;">nbegin</span><span class="o" style="font-weight: 600;">;</span></span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</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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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nloc</span><span class="o" style="font-weight: 600;">);</span></span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">();</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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702
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1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="java"><span class="o" style="font-weight: 600;">}</span></span>
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703
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1006
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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="java"></span></pre>
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<li id="e1a765a5b2b828119bc810319c6fa07e7300eecf">
<a href="https://salsa.debian.org/med-team/chromhmm/-/commit/bd1ced357ad13d08457efd9f61d467e43cd69cb6#e1a765a5b2b828119bc810319c6fa07e7300eecf"><strong>edu/mit/compbio/ChromHMM/ChromHMM.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1591" 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">@@ -1591,7 +1591,7 @@ public class ChromHMM</td>
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1591
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1591
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<pre style="margin: 0;"> <span id="LC1591" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>
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1592
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1592
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<pre style="margin: 0;"> <span id="LC1592" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1593
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1593
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<pre style="margin: 0;"> <span id="LC1593" class="line" lang="java"></span>
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1594
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<pre style="margin: 0;">-<span id="LC1594" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">s</span>tate ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" order)"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC1594" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">S</span>tate ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" order)"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC1595" 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;">ni</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;">ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">datasets</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;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>
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<pre style="margin: 0;"> <span id="LC1596" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC1597" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">datasets</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">colordering</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ni</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">@@ -1644,7 +1644,7 @@ public class ChromHMM</td>
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szfile</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC1647" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">s</span>tate (from\\to) ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" order)"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">S</span>tate (from\\to) ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" order)"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC1648" 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;">ni</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;">ni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numstates</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">++)</span></span>
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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+(</span><span class="n" style="color: #333;">ni</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">));</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12848" 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">@@ -12848,7 +12848,7 @@ public class ChromHMM</td>
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<pre style="margin: 0;"> <span id="LC12848" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC12849" 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;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Version"</span><span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;"> <span id="LC12850" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC12851" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"This is Version 1.2<span class="idiff left right">0</span> of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC12851" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"This is Version 1.2<span class="idiff left right">1</span> of ChromHMM (c) Copyright 2008-2012 Massachusetts Institute of Technology"</span><span class="o" style="font-weight: 600;">);</span></span>
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12852
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12852
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<pre style="margin: 0;"> <span id="LC12852" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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12853
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12853
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<pre style="margin: 0;"> <span id="LC12853" 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;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"BinarizeBam"</span><span class="o" style="font-weight: 600;">))||(</span><span class="n" style="color: #333;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"BinarizeBed"</span><span class="o" style="font-weight: 600;">)))</span></span>
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12854
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12854
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<pre style="margin: 0;"> <span id="LC12854" 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">@@ -13308,39 +13308,47 @@ public class ChromHMM</td>
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13308
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<pre style="margin: 0;"> <span id="LC13308" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bprintimage</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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13309
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13309
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<pre style="margin: 0;"> <span id="LC13309" class="line" lang="java"></span>
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13310
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13310
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<pre style="margin: 0;"> <span id="LC13310" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nargindex</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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13311
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<pre style="margin: 0;">-<span id="LC13311" 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;">args</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;">5</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC13311" class="line" lang="java"></span>
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13312
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<pre style="margin: 0;">+<span id="LC13312" 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;">args</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">)</span></span>
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13313
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<pre style="margin: 0;"> <span id="LC13313" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13314
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<pre style="margin: 0;"> <span id="LC13314" class="line" lang="java"> <span class="n" style="color: #333;">bok</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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<pre style="margin: 0;">-<span id="LC13314" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span></span>
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13315
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<pre style="margin: 0;">-<span id="LC13315" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC13316" 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;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-color"</span><span class="o" style="font-weight: 600;">))</span></span>
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13317
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<pre style="margin: 0;">-<span id="LC13317" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13318
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<pre style="margin: 0;">-<span id="LC13318" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcolor</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 class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">];</span></span>
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13319
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<pre style="margin: 0;">-<span id="LC13319" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolor</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolor</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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<pre style="margin: 0;">-<span id="LC13320" 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;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>
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13321
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<pre style="margin: 0;">-<span id="LC13321" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC13322" class="line" lang="java"> <span class="n" style="color: #333;">nr</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;">-<span id="LC13323" class="line" lang="java"> <span class="n" style="color: #333;">ng</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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13324
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<pre style="margin: 0;">-<span id="LC13324" class="line" lang="java"> <span class="n" style="color: #333;">nb</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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13325
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<pre style="margin: 0;">-<span id="LC13325" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13326
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<pre style="margin: 0;">-<span id="LC13326" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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13327
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<pre style="margin: 0;">-<span id="LC13327" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13328
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<pre style="margin: 0;">-<span id="LC13328" class="line" lang="java"> <span class="n" style="color: #333;">bok</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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13329
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<pre style="margin: 0;">-<span id="LC13329" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13330
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<pre style="margin: 0;">-<span id="LC13330" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13331
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<pre style="margin: 0;">-<span id="LC13331" 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;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-noimage"</span><span class="o" style="font-weight: 600;">))</span></span>
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13332
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<pre style="margin: 0;">-<span id="LC13332" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13333
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<pre style="margin: 0;">-<span id="LC13333" class="line" lang="java"> <span class="n" style="color: #333;">bprintimage</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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13334
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<pre style="margin: 0;">-<span id="LC13334" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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13335
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<pre style="margin: 0;">-<span id="LC13335" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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13336
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<pre style="margin: 0;">-<span id="LC13336" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13337
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<pre style="margin: 0;">-<span id="LC13337" class="line" lang="java"> <span class="n" style="color: #333;">bok</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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13338
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<pre style="margin: 0;">-<span id="LC13338" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13339
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<pre style="margin: 0;">-<span id="LC13339" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13340
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<pre style="margin: 0;">-<span id="LC13340" 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;">NumberFormatException</span> <span class="n" style="color: #333;">ex</span><span class="o" style="font-weight: 600;">)</span></span>
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13341
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<pre style="margin: 0;">-<span id="LC13341" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13342
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<pre style="margin: 0;">-<span id="LC13342" class="line" lang="java"> <span class="n" style="color: #333;">bok</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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13343
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<pre style="margin: 0;">-<span id="LC13343" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13315
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<pre style="margin: 0;">+<span id="LC13315" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13316
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<pre style="margin: 0;">+<span id="LC13316" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13317" 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">
13317
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<pre style="margin: 0;">+<span id="LC13317" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13318" 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">
13318
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<pre style="margin: 0;">+<span id="LC13318" class="line" lang="java"> <span class="k" style="font-weight: 600;">try</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13319" 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">
13319
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<pre style="margin: 0;">+<span id="LC13319" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="13344" 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="diff-line-num new new_line" data-linenumber="13320" 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">
13320
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<pre style="margin: 0;">+<span id="LC13320" 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;">nargindex</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 class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13321" 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">
13321
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<pre style="margin: 0;">+<span id="LC13321" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="13344" 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="diff-line-num new new_line" data-linenumber="13322" 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">
13322
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<pre style="margin: 0;">+<span id="LC13322" 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;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-color"</span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13323" 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">
13323
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<pre style="margin: 0;">+<span id="LC13323" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="13344" 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="diff-line-num new new_line" data-linenumber="13324" 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">
13324
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<pre style="margin: 0;">+<span id="LC13324" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcolor</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 class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13325" 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">
13325
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<pre style="margin: 0;">+<span id="LC13325" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">stcolor</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szcolor</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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<td class="diff-line-num new new_line" data-linenumber="13326" 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">
13326
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<pre style="margin: 0;">+<span id="LC13326" 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;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">countTokens</span><span class="o" style="font-weight: 600;">()==</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13327" 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">
13327
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<pre style="margin: 0;">+<span id="LC13327" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13328" 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">
13328
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<pre style="margin: 0;">+<span id="LC13328" class="line" lang="java"> <span class="n" style="color: #333;">nr</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13329" 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">
13329
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<pre style="margin: 0;">+<span id="LC13329" class="line" lang="java"> <span class="n" style="color: #333;">ng</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13330" 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">
13330
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<pre style="margin: 0;">+<span id="LC13330" class="line" lang="java"> <span class="n" style="color: #333;">nb</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">stcolor</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13331" 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">
13331
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<pre style="margin: 0;">+<span id="LC13331" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13332" 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">
13332
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<pre style="margin: 0;">+<span id="LC13332" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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13333
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<pre style="margin: 0;">+<span id="LC13333" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13334" 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">
13334
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<pre style="margin: 0;">+<span id="LC13334" class="line" lang="java"> <span class="n" style="color: #333;">bok</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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13335
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<pre style="margin: 0;">+<span id="LC13335" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13336
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<pre style="margin: 0;">+<span id="LC13336" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13337
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<pre style="margin: 0;">+<span id="LC13337" 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;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-noimage"</span><span class="o" style="font-weight: 600;">))</span></span>
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13338
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<pre style="margin: 0;">+<span id="LC13338" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13339
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<pre style="margin: 0;">+<span id="LC13339" class="line" lang="java"> <span class="n" style="color: #333;">bprintimage</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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13340
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<pre style="margin: 0;">+<span id="LC13340" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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13341
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<pre style="margin: 0;">+<span id="LC13341" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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13342
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<pre style="margin: 0;">+<span id="LC13342" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13343
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<pre style="margin: 0;">+<span id="LC13343" class="line" lang="java"> <span class="n" style="color: #333;">bok</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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13344
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<pre style="margin: 0;">+<span id="LC13344" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13345
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<pre style="margin: 0;">+<span id="LC13345" class="line" lang="java"> <span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">++;</span></span>
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13346
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<pre style="margin: 0;">+<span id="LC13346" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13347
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<pre style="margin: 0;">+<span id="LC13347" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13348
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<pre style="margin: 0;">+<span id="LC13348" 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;">NumberFormatException</span> <span class="n" style="color: #333;">ex</span><span class="o" style="font-weight: 600;">)</span></span>
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13349
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<pre style="margin: 0;">+<span id="LC13349" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC13350" class="line" lang="java"> <span class="n" style="color: #333;">bok</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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13351
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<pre style="margin: 0;">+<span id="LC13351" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13344
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13352
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<pre style="margin: 0;"> <span id="LC13352" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13353
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<pre style="margin: 0;"> <span id="LC13353" class="line" lang="java"> </span>
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13346
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13354
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<pre style="margin: 0;"> <span id="LC13354" 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;">nargindex</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 class="na" style="color: #008080;">length</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13476" 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">@@ -13476,7 +13484,7 @@ public class ChromHMM</td>
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13476
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13484
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<pre style="margin: 0;"> <span id="LC13484" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13477
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13485
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<pre style="margin: 0;"> <span id="LC13485" class="line" lang="java"> <span class="n" style="color: #333;">breadposterior</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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13478
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13486
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<pre style="margin: 0;"> <span id="LC13486" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13479
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<pre style="margin: 0;">-<span id="LC13479" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">nargindex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"-readstatesbyline"</span></span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13487" 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">
13487
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<pre style="margin: 0;">+<span id="LC13487" 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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">nargindex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-readstatesbyline"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">))||(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">nargindex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-readstatebyline"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>))</span></span>
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13480
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13488
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<pre style="margin: 0;"> <span id="LC13488" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13481
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<td class="diff-line-num new_line" data-linenumber="13489" 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">
13489
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<pre style="margin: 0;"> <span id="LC13489" class="line" lang="java"> <span class="n" style="color: #333;">breadstatebyline</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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13482
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13490
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<pre style="margin: 0;"> <span id="LC13490" class="line" lang="java"> <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="13602" 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="13610" 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">@@ -13602,7 +13610,7 @@ public class ChromHMM</td>
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13602
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13610
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<pre style="margin: 0;"> <span id="LC13610" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13603
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<td class="diff-line-num new_line" data-linenumber="13611" 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">
13611
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<pre style="margin: 0;"> <span id="LC13611" class="line" lang="java"> <span class="n" style="color: #333;">bprintposterior</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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<td class="diff-line-num old_line" data-linenumber="13604" 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">
13604
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<td class="diff-line-num new_line" data-linenumber="13612" 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">
13612
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<pre style="margin: 0;"> <span id="LC13612" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="13605" 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">
13605
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<td class="diff-line-num new_line old" data-linenumber="13613" 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="LC13605" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">nargindex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"-printstatesbyline"</span></span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13613" 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">
13613
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<pre style="margin: 0;">+<span id="LC13613" 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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">nargindex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-printstatesbyline"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">))||(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">nargindex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-printstatebyline"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>))</span></span>
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13606
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13614
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<pre style="margin: 0;"> <span id="LC13614" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13607
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13615
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<pre style="margin: 0;"> <span id="LC13615" class="line" lang="java"> <span class="n" style="color: #333;">bprintstatebyline</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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13608
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13616
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<pre style="margin: 0;"> <span id="LC13616" class="line" lang="java"> <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="13694" 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="13702" 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">@@ -13694,7 +13702,7 @@ public class ChromHMM</td>
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13694
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13702
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<pre style="margin: 0;"> <span id="LC13702" 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;">bok</span><span class="o" style="font-weight: 600;">)</span></span>
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13695
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13703
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<pre style="margin: 0;"> <span id="LC13703" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13696
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13704
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<pre style="margin: 0;"> <span id="LC13704" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"usage: MakeSegmentation [-b binsize][-f inputfilelist][-gzip][-i outfileID][-l chromosomelengthfile][-lowmem][-many][-nobed]"</span><span class="o" style="font-weight: 600;">+</span></span>
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13697
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<pre style="margin: 0;">-<span id="LC13697" class="line" lang="java"> <span class="s" style="color: #d14;">"[-printposterior][-printstate<span class="idiff left right">s</span>byline][-scalebeta][-splitrows]"</span><span class="o" style="font-weight: 600;">+</span></span>
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13705
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<pre style="margin: 0;">+<span id="LC13705" class="line" lang="java"> <span class="s" style="color: #d14;">"[-printposterior][-printstatebyline][-scalebeta][-splitrows]"</span><span class="o" style="font-weight: 600;">+</span></span>
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13698
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13706
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<pre style="margin: 0;"> <span id="LC13706" class="line" lang="java"> <span class="s" style="color: #d14;">" modelfile inputdir outputdir"</span><span class="o" style="font-weight: 600;">);</span></span>
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13699
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13707
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<pre style="margin: 0;"> <span id="LC13707" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13700
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13708
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<pre style="margin: 0;"> <span id="LC13708" class="line" lang="java"> <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="13703" 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="13711" 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">@@ -13703,7 +13711,7 @@ public class ChromHMM</td>
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13703
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13711
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<pre style="margin: 0;"> <span id="LC13711" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szcolormapping</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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13704
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13712
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<pre style="margin: 0;"> <span id="LC13712" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szlabelmapping</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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13705
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13713
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<pre style="margin: 0;"> <span id="LC13713" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="n" style="color: #333;">bgzip</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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13706
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<td class="diff-line-num new_line old" data-linenumber="13714" 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="LC13706" class="line" lang="java"> </span>
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13714
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<pre style="margin: 0;">+<span id="LC13714" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">blowmem</span></span><span class="idiff"> </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">false</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">;</span></span></span>
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13707
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13715
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<pre style="margin: 0;"> <span id="LC13715" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nargindex</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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13708
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13716
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<pre style="margin: 0;"> <span id="LC13716" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numstates</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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13709
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13717
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<pre style="margin: 0;"> <span id="LC13717" class="line" lang="java"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13722" 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="13730" 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">@@ -13722,6 +13730,10 @@ public class ChromHMM</td>
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13722
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13730
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<pre style="margin: 0;"> <span id="LC13730" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//the -l is for backwards compatibility</span></span>
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13723
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13731
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<pre style="margin: 0;"> <span id="LC13731" class="line" lang="java"> <span class="n" style="color: #333;">szlabelmapping</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 class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">];</span></span>
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13724
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13732
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<pre style="margin: 0;"> <span id="LC13732" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13733" 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">
13733
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<pre style="margin: 0;">+<span id="LC13733" 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;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-lowmem"</span><span class="o" style="font-weight: 600;">))</span></span>
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13734
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<pre style="margin: 0;">+<span id="LC13734" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13735
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<pre style="margin: 0;">+<span id="LC13735" class="line" lang="java"> <span class="n" style="color: #333;">blowmem</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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13736
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<pre style="margin: 0;">+<span id="LC13736" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13725
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13737
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<pre style="margin: 0;"> <span id="LC13737" 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;">args</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nargindex</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"-n"</span><span class="o" style="font-weight: 600;">))</span></span>
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13726
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13738
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<pre style="margin: 0;"> <span id="LC13738" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13727
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13739
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<pre style="margin: 0;"> <span id="LC13739" class="line" lang="java"> <span class="n" style="color: #333;">numstates</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;">parseInt</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 class="n" style="color: #333;">nargindex</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">@@ -13742,7 +13754,14 @@ public class ChromHMM</td>
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13742
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<pre style="margin: 0;"> <span id="LC13754" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BrowserOutput</span> <span class="n" style="color: #333;">theBrowserOutput</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;">BrowserOutput</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szsegmentfile</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szcolormapping</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szlabelmapping</span><span class="o" style="font-weight: 600;">,</span></span>
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13743
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13755
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<pre style="margin: 0;"> <span id="LC13755" class="line" lang="java"> <span class="n" style="color: #333;">szsegmentationname</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">szoutputfileprefix</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">numstates</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bgzip</span><span class="o" style="font-weight: 600;">);</span></span>
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13744
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13756
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<pre style="margin: 0;"> <span id="LC13756" class="line" lang="java"> <span class="n" style="color: #333;">theBrowserOutput</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makebrowserdense</span><span class="o" style="font-weight: 600;">();</span></span>
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13745
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<pre style="margin: 0;">-<span id="LC13745" class="line" lang="java"> <span class="n" style="color: #333;">theBrowserOutput</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makebrowserexpanded</span><span class="o" style="font-weight: 600;">();</span></span>
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13757
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<pre style="margin: 0;">+<span id="LC13757" 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;">blowmem</span><span class="o" style="font-weight: 600;">)</span></span>
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13758
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<pre style="margin: 0;">+<span id="LC13758" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13759
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<pre style="margin: 0;">+<span id="LC13759" class="line" lang="java"> <span class="n" style="color: #333;">theBrowserOutput</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makebrowserexpandedLowMem</span><span class="o" style="font-weight: 600;">();</span></span>
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13760
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<pre style="margin: 0;">+<span id="LC13760" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13761
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<pre style="margin: 0;">+<span id="LC13761" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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13762
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<pre style="margin: 0;">+<span id="LC13762" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13763
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<pre style="margin: 0;">+<span id="LC13763" class="line" lang="java"> <span class="n" style="color: #333;">theBrowserOutput</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makebrowserexpanded</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC13764" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC13765" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13766
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<pre style="margin: 0;"> <span id="LC13766" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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13767
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<pre style="margin: 0;"> <span id="LC13767" 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">@@ -13751,7 +13770,7 @@ public class ChromHMM</td>
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13770
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<pre style="margin: 0;"> <span id="LC13770" class="line" lang="java"> </span>
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13771
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<pre style="margin: 0;"> <span id="LC13771" 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;">bok</span><span class="o" style="font-weight: 600;">)</span></span>
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13772
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<pre style="margin: 0;"> <span id="LC13772" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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13754
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<pre style="margin: 0;">-<span id="LC13754" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"usage: MakeBrowserFiles [-c colormappingfile][-gzip][-m labelmappingfile][-n numstates] segmentfile segmentationname outputfileprefix"</span><span class="o" style="font-weight: 600;">);</span></span>
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13773
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<pre style="margin: 0;">+<span id="LC13773" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"usage: MakeBrowserFiles [-c colormappingfile][-gzip][-<span class="idiff left right">lowmem][-</span>m labelmappingfile][-n numstates] segmentfile segmentationname outputfileprefix"</span><span class="o" style="font-weight: 600;">);</span></span>
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13774
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<pre style="margin: 0;"> <span id="LC13774" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13756
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13775
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<pre style="margin: 0;"> <span id="LC13775" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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13757
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13776
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<pre style="margin: 0;"> <span id="LC13776" 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;">szcommand</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equalsIgnoreCase</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"OverlapEnrichment"</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="14342" 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">@@ -14323,7 +14342,7 @@ public class ChromHMM</td>
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14323
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14342
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<pre style="margin: 0;"> <span id="LC14342" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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14324
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14343
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<pre style="margin: 0;"> <span id="LC14343" class="line" lang="java"> <span class="n" style="color: #333;">bnoorderrows</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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14325
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<td class="diff-line-num new_line" data-linenumber="14344" 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">
14344
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<pre style="margin: 0;"> <span id="LC14344" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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14326
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<td class="diff-line-num new_line old" data-linenumber="14345" 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="LC14326" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">nargindex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"-printstatebyline"</span></span><span class="o" style="font-weight: 600;">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14345" 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">
14345
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<pre style="margin: 0;">+<span id="LC14345" 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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">nargindex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-printstatebyline"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">))||(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">nargindex</span></span><span class="o" style="font-weight: 600;"><span class="idiff">].</span></span><span class="na" style="color: #008080;"><span class="idiff">equals</span></span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"-printstatesbyline"</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">)</span>))</span></span>
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14327
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14346
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<pre style="margin: 0;"> <span id="LC14346" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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14328
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14347
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<pre style="margin: 0;"> <span id="LC14347" class="line" lang="java"> <span class="n" style="color: #333;">bprintstatebyline</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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14329
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14348
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<pre style="margin: 0;"> <span id="LC14348" class="line" lang="java"> <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="14559" 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="14578" 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">@@ -14559,7 +14578,14 @@ public class ChromHMM</td>
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14559
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14578
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<pre style="margin: 0;"> <span id="LC14578" class="line" lang="java"> <span class="n" style="color: #333;">szprefix</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">szoutputdir</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;">szprefix</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">numstates</span><span class="o" style="font-weight: 600;">,</span><span class="n" style="color: #333;">bgzip</span><span class="o" style="font-weight: 600;">);</span></span>
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14560
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14579
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<pre style="margin: 0;"> <span id="LC14579" class="line" lang="java"></span>
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14561
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14580
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<pre style="margin: 0;"> <span id="LC14580" class="line" lang="java"> <span class="n" style="color: #333;">theBrowserOutput</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makebrowserdense</span><span class="o" style="font-weight: 600;">();</span></span>
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14562
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<td class="diff-line-num new_line old" data-linenumber="14581" 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="LC14562" class="line" lang="java"> <span class="n" style="color: #333;">theBrowserOutput</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makebrowserexpanded</span><span class="o" style="font-weight: 600;">();</span></span>
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14581
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<pre style="margin: 0;">+<span id="LC14581" 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;">blowmem</span><span class="o" style="font-weight: 600;">)</span></span>
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14582
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<pre style="margin: 0;">+<span id="LC14582" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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14583
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<pre style="margin: 0;">+<span id="LC14583" class="line" lang="java"> <span class="n" style="color: #333;">theBrowserOutput</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makebrowserexpandedLowMem</span><span class="o" style="font-weight: 600;">();</span></span>
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14584
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<pre style="margin: 0;">+<span id="LC14584" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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14585
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<pre style="margin: 0;">+<span id="LC14585" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC14586" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC14587" class="line" lang="java"> <span class="n" style="color: #333;">theBrowserOutput</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">makebrowserexpanded</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;">+<span id="LC14588" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC14589" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC14590" 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;">bgzip</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC14591" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<a href="https://salsa.debian.org/med-team/chromhmm/-/commit/bd1ced357ad13d08457efd9f61d467e43cd69cb6#7e91b8c750d2f1f3056fc7dcbd7d4d639572d170"><strong>edu/mit/compbio/ChromHMM/Preprocessing.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">@@ -2487,6 +2487,12 @@ public class Preprocessing</td>
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<pre style="margin: 0;"> <span id="LC2487" class="line" lang="java"> <span class="n" style="color: #333;">nfilecount</span><span class="o" style="font-weight: 600;">++;</span></span>
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<pre style="margin: 0;"> <span id="LC2488" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC2489" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC2490" class="line" lang="java"></span>
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<pre style="margin: 0;">+<span id="LC2491" 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;">nfilecount</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="LC2492" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC2493" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No _signal files were found in directory "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szbinneddataDIR</span><span class="o" style="font-weight: 600;">);</span></span>
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2494
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<pre style="margin: 0;">+<span id="LC2494" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC2495" class="line" lang="java"></span>
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2496
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<pre style="margin: 0;"> <span id="LC2496" 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;">signalchromfiles</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;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfilecount</span><span class="o" style="font-weight: 600;">];</span></span>
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2491
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2497
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<pre style="margin: 0;"> <span id="LC2497" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfileindex</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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2492
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2498
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<pre style="margin: 0;"> <span id="LC2498" 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;">nfile</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;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">allfiles</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;">nfile</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="3116" 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">@@ -3110,6 +3116,12 @@ public class Preprocessing</td>
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3110
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3116
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<pre style="margin: 0;"> <span id="LC3116" class="line" lang="java"> <span class="n" style="color: #333;">nfilecount</span><span class="o" style="font-weight: 600;">++;</span></span>
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3117
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<pre style="margin: 0;"> <span id="LC3117" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3118
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<pre style="margin: 0;"> <span id="LC3118" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3119
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<pre style="margin: 0;">+<span id="LC3119" class="line" lang="java"></span>
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<td class="diff-line-num new new_line" data-linenumber="3120" 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">
3120
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<pre style="margin: 0;">+<span id="LC3120" 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;">nfilecount</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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3121
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<pre style="margin: 0;">+<span id="LC3121" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3122" 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">
3122
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<pre style="margin: 0;">+<span id="LC3122" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"No _signal files were found in directory "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szbinneddataDIR</span><span class="o" style="font-weight: 600;">);</span></span>
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3123
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<pre style="margin: 0;">+<span id="LC3123" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3124
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<pre style="margin: 0;">+<span id="LC3124" class="line" lang="java"></span>
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3113
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3125
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<pre style="margin: 0;"> <span id="LC3125" 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;">signalchromfiles</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;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfilecount</span><span class="o" style="font-weight: 600;">];</span></span>
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3114
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3126
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<pre style="margin: 0;"> <span id="LC3126" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfileindex</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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3115
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3127
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<pre style="margin: 0;"> <span id="LC3127" 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;">nfile</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;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">allfiles</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;">nfile</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="3979" 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="3991" 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">@@ -3979,7 +3991,10 @@ public class Preprocessing</td>
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3979
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3991
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<pre style="margin: 0;"> <span id="LC3991" 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;">ndir</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;">ndir</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">hmbrA</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;">ndir</span><span class="o" style="font-weight: 600;">++)</span></span>
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3980
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3992
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<pre style="margin: 0;"> <span id="LC3992" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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3981
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3993
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<pre style="margin: 0;"> <span id="LC3993" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span> <span class="n" style="color: #333;">br</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;">BufferedReader</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">hmbrA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ndir</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;">szcurrfile</span><span class="o" style="font-weight: 600;">);</span></span>
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3982
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<pre style="margin: 0;">-<span id="LC3982" class="line" lang="java"> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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3994
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<pre style="margin: 0;">+<span id="LC3994" 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;">br</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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3995
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<pre style="margin: 0;">+<span id="LC3995" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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3996
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<pre style="margin: 0;">+<span id="LC3996" class="line" lang="java"> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">close</span><span class="o" style="font-weight: 600;">();</span></span>
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3997
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<pre style="margin: 0;">+<span id="LC3997" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3983
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3998
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<pre style="margin: 0;"> <span id="LC3998" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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3984
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3999
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<pre style="margin: 0;"> <span id="LC3999" class="line" lang="java"></span>
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3985
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4000
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<pre style="margin: 0;"> <span id="LC4000" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<a href="https://salsa.debian.org/med-team/chromhmm/-/commit/bd1ced357ad13d08457efd9f61d467e43cd69cb6#4fb31ca7c49b2c49cfd549091ba94777db11f494"><strong>edu/mit/compbio/ChromHMM/StateAnalysis.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">@@ -685,13 +685,23 @@ public class StateAnalysis</td>
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span> <span class="n" style="color: #333;">brinputsegment</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szinputsegment</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC686" 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;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brinputsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</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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<pre style="margin: 0;"> <span id="LC687" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC689" 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;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> </span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegincoord</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendcoord</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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<pre style="margin: 0;"> <span id="LC701" 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;">nbegincoord</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">nbinsize</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="LC702" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Binsize of "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" does not agree with input segment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">);</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Binsize of "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" does not agree with coordinates in input segment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">". -b binsize should match parameter value to LearnModel or "</span><span class="o" style="font-weight: 600;">+</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="java"> <span class="s" style="color: #d14;">"MakeSegmentation used to produce segmentation. If segmentation is derived from a lift over from another assembly, then the '-b 1' option should be used"</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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706
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nbegincoord</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">;</span></span>
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697
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nendcoord</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</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">@@ -1289,13 +1299,23 @@ public class StateAnalysis</td>
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1289
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1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">BufferedReader</span> <span class="n" style="color: #333;">brinputsegment</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szinputsegment</span><span class="o" style="font-weight: 600;">);</span></span>
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1290
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1300
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<pre style="margin: 0;"> <span id="LC1300" 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;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brinputsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</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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1291
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1301
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1292
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<pre style="margin: 0;">-<span id="LC1292" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">;</span></span>
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1303
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<pre style="margin: 0;">+<span id="LC1303" 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;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>
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1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="java"></span>
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1293
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1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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1294
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1313
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbegincoord</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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1295
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1314
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<pre style="margin: 0;"> <span id="LC1314" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nendcoord</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;">parseInt</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">());</span></span>
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1296
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1315
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<pre style="margin: 0;"> <span id="LC1315" 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;">nbegincoord</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">nbinsize</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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1297
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1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1298
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<td class="diff-line-num new_line old" data-linenumber="1317" 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="LC1298" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Binsize of "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" does not agree with input segment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">);</span></span>
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1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">IllegalArgumentException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Binsize of "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">nbinsize</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" does not agree with coordinates in input segment "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">". -b binsize should match parameter value to LearnModel or "</span><span class="o" style="font-weight: 600;">+</span></span>
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1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="java"> <span class="s" style="color: #d14;">"MakeSegmentation used to produce segmentation. If segmentation is derived from a lift over from another assembly, then the '-b 1' option should be used"</span><span class="o" style="font-weight: 600;">);</span></span>
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1299
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1319
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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1300
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1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//int nbegin = nbegincoord/nbinsize;</span></span>
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1301
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1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nend</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">nendcoord</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)/</span><span class="n" style="color: #333;">nbinsize</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="1431" 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="1451" 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">@@ -1431,7 +1451,16 @@ public class StateAnalysis</td>
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1431
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1451
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<pre style="margin: 0;"> <span id="LC1451" class="line" lang="java"> <span class="n" style="color: #333;">brinputsegment</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Util</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getBufferedReader</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szinputsegment</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1432" 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">
1432
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<td class="diff-line-num new_line" data-linenumber="1452" 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">
1452
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<pre style="margin: 0;"> <span id="LC1452" 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;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brinputsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</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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1433
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1453
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<pre style="margin: 0;"> <span id="LC1453" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1434
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<pre style="margin: 0;">-<span id="LC1434" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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1454
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">;</span></span>
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1455
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<pre style="margin: 0;">+<span id="LC1455" 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;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>
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1456
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<pre style="margin: 0;">+<span id="LC1456" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1457
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<pre style="margin: 0;">+<span id="LC1457" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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1458
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<pre style="margin: 0;">+<span id="LC1458" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1459
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<pre style="margin: 0;">+<span id="LC1459" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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1460
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<pre style="margin: 0;">+<span id="LC1460" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1461
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<pre style="margin: 0;">+<span id="LC1461" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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1462
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<pre style="margin: 0;">+<span id="LC1462" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1463
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="java"></span>
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1435
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1464
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<pre style="margin: 0;"> <span id="LC1464" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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1436
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1465
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<pre style="margin: 0;"> <span id="LC1465" 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;">szchrom</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchromwant</span><span class="o" style="font-weight: 600;">))</span> </span>
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1437
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1466
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<pre style="margin: 0;"> <span id="LC1466" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</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="1862" 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="1891" 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">@@ -1862,7 +1891,7 @@ public class StateAnalysis</td>
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1891
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<pre style="margin: 0;"> <span id="LC1891" class="line" lang="java"> <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;">out</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">println</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"Writing to file "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".txt"</span><span class="o" style="font-weight: 600;">);</span></span>
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1863
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1892
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<pre style="margin: 0;"> <span id="LC1892" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">PrintWriter</span> <span class="n" style="color: #333;">pw</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;">PrintWriter</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;">FileWriter</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szoutfile</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">".txt"</span><span class="o" style="font-weight: 600;">));</span></span>
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1864
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1893
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<pre style="margin: 0;"> <span id="LC1893" class="line" lang="java"></span>
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1865
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<td class="diff-line-num new_line old" data-linenumber="1894" 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="LC1865" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">s</span>tate ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szstateorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" order)\tGenome %"</span><span class="o" style="font-weight: 600;">);</span></span>
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1894
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<pre style="margin: 0;">+<span id="LC1894" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">S</span>tate ("</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">szstateorder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" order)\tGenome %"</span><span class="o" style="font-weight: 600;">);</span></span>
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1866
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1895
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<pre style="margin: 0;"> <span id="LC1895" 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;">nfile</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;">nfile</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">files</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;">nfile</span><span class="o" style="font-weight: 600;">++)</span></span>
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1867
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1896
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<pre style="margin: 0;"> <span id="LC1896" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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1868
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1897
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<pre style="margin: 0;"> <span id="LC1897" class="line" lang="java"> <span class="n" style="color: #333;">pw</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">nfile</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="2209" 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="2238" 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">@@ -2209,7 +2238,15 @@ public class StateAnalysis</td>
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2209
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2238
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<pre style="margin: 0;"> <span id="LC2238" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//this loops reads in the segmentation </span></span>
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2210
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2239
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<pre style="margin: 0;"> <span id="LC2239" 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;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brinputsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</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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2211
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2240
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<pre style="margin: 0;"> <span id="LC2240" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2212
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<pre style="margin: 0;">-<span id="LC2212" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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2241
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<pre style="margin: 0;">+<span id="LC2241" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">;</span></span>
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2242
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<pre style="margin: 0;">+<span id="LC2242" 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;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>
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2243
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<pre style="margin: 0;">+<span id="LC2243" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2244
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<pre style="margin: 0;">+<span id="LC2244" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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2245
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<pre style="margin: 0;">+<span id="LC2245" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2246
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<pre style="margin: 0;">+<span id="LC2246" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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2247
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<pre style="margin: 0;">+<span id="LC2247" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2248
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<pre style="margin: 0;">+<span id="LC2248" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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2249
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<pre style="margin: 0;">+<span id="LC2249" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2213
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2250
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<pre style="margin: 0;"> <span id="LC2250" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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2214
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2251
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<pre style="margin: 0;"> <span id="LC2251" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//assumes segments are in standard bed format which to get to </span></span>
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2215
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2252
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<pre style="margin: 0;"> <span id="LC2252" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//0-based inclusive requires substract 1 from the end</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2356" 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">@@ -2356,8 +2393,16 @@ public class StateAnalysis</td>
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2356
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2393
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<pre style="margin: 0;"> <span id="LC2393" 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;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brinputsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</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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2357
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2394
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<pre style="margin: 0;"> <span id="LC2394" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2358
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2395
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<pre style="margin: 0;"> <span id="LC2395" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//int numlines = alsegments.size();</span></span>
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2396
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<pre style="margin: 0;">+<span id="LC2396" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">;</span></span>
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2397
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<pre style="margin: 0;">+<span id="LC2397" 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;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>
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2398
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<pre style="margin: 0;">+<span id="LC2398" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC2399" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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2400
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<pre style="margin: 0;">+<span id="LC2400" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2401
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<pre style="margin: 0;">+<span id="LC2401" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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2402
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<pre style="margin: 0;">+<span id="LC2402" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2403
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<pre style="margin: 0;">+<span id="LC2403" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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2404
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<pre style="margin: 0;">+<span id="LC2404" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2405
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<pre style="margin: 0;"> <span id="LC2405" class="line" lang="java"></span>
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2360
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<pre style="margin: 0;">-<span id="LC2360" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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2361
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2406
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<pre style="margin: 0;"> <span id="LC2406" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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2362
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2407
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<pre style="margin: 0;"> <span id="LC2407" 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;">szchromwant</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">equals</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szchrom</span><span class="o" style="font-weight: 600;">))</span></span>
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2363
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2408
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<pre style="margin: 0;"> <span id="LC2408" class="line" lang="java"> <span class="k" style="font-weight: 600;">continue</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="2591" 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">@@ -2591,7 +2636,15 @@ public class StateAnalysis</td>
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2636
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<pre style="margin: 0;"> <span id="LC2636" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//this loops reads in the segmentation </span></span>
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2592
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2637
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<pre style="margin: 0;"> <span id="LC2637" 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;">szLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">brinputsegment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">readLine</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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2593
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2638
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<pre style="margin: 0;"> <span id="LC2638" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2594
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<pre style="margin: 0;">-<span id="LC2594" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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2639
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<pre style="margin: 0;">+<span id="LC2639" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">StringTokenizer</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">;</span></span>
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2640
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<pre style="margin: 0;">+<span id="LC2640" 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;">bstringlabels</span><span class="o" style="font-weight: 600;">)</span></span>
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2641
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<pre style="margin: 0;">+<span id="LC2641" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2642
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<pre style="margin: 0;">+<span id="LC2642" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t"</span><span class="o" style="font-weight: 600;">);</span></span>
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2643
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<pre style="margin: 0;">+<span id="LC2643" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2644
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<pre style="margin: 0;">+<span id="LC2644" class="line" lang="java"> <span class="k" style="font-weight: 600;">else</span></span>
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2645
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<pre style="margin: 0;">+<span id="LC2645" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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2646
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<pre style="margin: 0;">+<span id="LC2646" class="line" lang="java"> <span class="n" style="color: #333;">st</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;">StringTokenizer</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">szLine</span><span class="o" style="font-weight: 600;">,</span><span class="s" style="color: #d14;">"\t "</span><span class="o" style="font-weight: 600;">);</span></span>
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2647
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<pre style="margin: 0;">+<span id="LC2647" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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2595
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2648
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<pre style="margin: 0;"> <span id="LC2648" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">szchrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nextToken</span><span class="o" style="font-weight: 600;">();</span></span>
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2596
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2649
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<pre style="margin: 0;"> <span id="LC2649" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//assumes segments are in standard bed format which to get to </span></span>
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2597
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2650
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<pre style="margin: 0;"> <span id="LC2650" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">//0-based inclusive requires substract 1 from the end</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3785" 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">@@ -3785,7 +3838,7 @@ public class StateAnalysis</td>
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3785
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3838
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<pre style="margin: 0;"> <span id="LC3838" 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;">collabels</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;">String</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">theRecEmissionFileCompareA</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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3786
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3839
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<pre style="margin: 0;"> <span id="LC3839" class="line" lang="java"></span>
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3787
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3840
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<pre style="margin: 0;"> <span id="LC3840" class="line" lang="java"></span>
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3788
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<pre style="margin: 0;">-<span id="LC3788" class="line" lang="java"> <span class="n" style="color: #333;">pwcompare</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">s</span>tate"</span><span class="o" style="font-weight: 600;">);</span></span>
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3841
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<pre style="margin: 0;">+<span id="LC3841" class="line" lang="java"> <span class="n" style="color: #333;">pwcompare</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">print</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"<span class="idiff left right">S</span>tate"</span><span class="o" style="font-weight: 600;">);</span></span>
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3789
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3842
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<pre style="margin: 0;"> <span id="LC3842" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ncol</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;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">theRecEmissionFileCompareA</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;">ncol</span><span class="o" style="font-weight: 600;">++)</span></span>
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3790
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3843
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<pre style="margin: 0;"> <span id="LC3843" class="line" lang="java"> <span class="o" style="font-weight: 600;">{</span></span>
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3791
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3844
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<pre style="margin: 0;"> <span id="LC3844" class="line" lang="java"> <span class="n" style="color: #333;">collabels</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">]</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;">theRecEmissionFileCompareA</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">].</span><span class="na" style="color: #008080;">numstates</span><span class="o" style="font-weight: 600;">;</span></span>
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