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<h3>
Étienne Mollier pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bbmap">Debian Med / bbmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/bbmap/-/commit/d4520373ab54d86278cb3713e4addaba8d2d8f0d">d4520373</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2022-03-05T12:35:43+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 38.96+dfsg</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#57363d0830f19d81c2022a5eb5019ed7ab89fe0a">
bbmap.sh
</a>
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<li class="file-stats">
<a href="#92cceaf1936602cf0e945d5b67fd49f518f99eb3">
current/align2/AbstractMapThread.java
</a>
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<li class="file-stats">
<a href="#ef3b3e694c0bbaa70bf4c35a23c328ce44020fb6">
current/shared/Shared.java
</a>
</li>
<li class="file-stats">
<a href="#4e3d7fe28dc46e7f8ac37caf3057c12574899ec3">
current/stream/ReadStreamByteWriter.java
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</li>
</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/bbmap/-/commit/d4520373ab54d86278cb3713e4addaba8d2d8f0d#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,4 +3,4 @@</td>
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Language: Java, Bash</span></span>
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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Information about documentation is in /docs/readme.txt.</span></span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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6
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<td class="new_line diff-line-num old" data-linenumber="6" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Version 38.9<span class="idiff left right deletion">5</span></span></span></pre></td>
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<td class="old_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" 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">
6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Version 38.9<span class="idiff left right addition">6</span></span></span></pre></td>
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<li id="57363d0830f19d81c2022a5eb5019ed7ab89fe0a">
<a href="https://salsa.debian.org/med-team/bbmap/-/commit/d4520373ab54d86278cb3713e4addaba8d2d8f0d#57363d0830f19d81c2022a5eb5019ed7ab89fe0a"><strong>bbmap.sh</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" 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">@@ -4,7 +4,7 @@ usage(){</td>
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span></span>
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<td class="new_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="s2" style="color: #d14;">BBMap</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">Written by Brian Bushnell, from Dec. 2010 - present</span></span>
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<td class="old_line diff-line-num old" data-linenumber="7" 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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<td class="new_line diff-line-num old" data-linenumber="7" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified February <span class="idiff left deletion">13</span>, 202<span class="idiff right deletion">0</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="s2" style="color: #d14;">Last modified February <span class="idiff left addition">24</span>, 202<span class="idiff right addition">2</span></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"></span>
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="s2" style="color: #d14;">Description: Fast and accurate splice-aware read aligner.</span></span>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">Please read bbmap/docs/guides/BBMapGuide.txt for more information.</span></span>
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<li id="92cceaf1936602cf0e945d5b67fd49f518f99eb3">
<a href="https://salsa.debian.org/med-team/bbmap/-/commit/d4520373ab54d86278cb3713e4addaba8d2d8f0d#92cceaf1936602cf0e945d5b67fd49f518f99eb3"><strong>current/align2/AbstractMapThread.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="970" 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="970" 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">@@ -970,7 +970,6 @@ public abstract class AbstractMapThread extends Thread {</td>
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970
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970
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC970" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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971
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971
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC971" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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972
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972
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC972" class="line" lang="java"> </span>
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973
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC973" class="line" lang="java"> </span>
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974
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973
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC973" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">SiteScore</span> <span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">topSite</span><span class="o" style="font-weight: 600;">();</span></span>
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975
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974
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC974" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">topSite</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC975" class="line" lang="java"> </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">@@ -1343,11 +1342,14 @@ public abstract class AbstractMapThread extends Thread {</td>
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1342
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1342" 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;">printSecondary</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">numSites</span><span class="o" style="font-weight: 600;">()<</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">){</span><span class="k" style="font-weight: 600;">return</span><span class="o" style="font-weight: 600;">;}</span></span>
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1344
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1343
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1343" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">topSite</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">slowScore</span><span class="o" style="font-weight: 600;">;</span></span>
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1345
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1344
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1344" class="line" lang="java"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">min</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">500</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="n" style="color: #333;">max</span><span class="o" style="font-weight: 600;">*</span><span class="no" style="color: #008080;">SECONDARY_SITE_SCORE_RATIO</span><span class="o" style="font-weight: 600;">));</span></span>
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1345
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1345" class="line" lang="java"> </span>
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1346
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1346" 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;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ambiguous</span><span class="o" style="font-weight: 600;">()){</span><span class="c1" style="color: #998; font-style: italic;">//Ensures ambiguous reads will have at least one secondary site</span></span>
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<td class="new_line diff-line-num old" data-linenumber="1347" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1347" class="line" lang="java"> <span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">m<span class="idiff left right deletion">ax</span></span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sites</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;">1</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">score</span><span class="o" style="font-weight: 600;">);</span></span>
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1347
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1347" class="line" lang="java"> <span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">m<span class="idiff left addition">in</span></span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sites</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;">1</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">s<span class="idiff right addition">lowS</span>core</span><span class="o" style="font-weight: 600;">);</span></span>
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1348
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1348
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1348" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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1349
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1349
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1349" class="line" lang="java"> <span class="k" style="font-weight: 600;">for</span><span class="o" style="font-weight: 600;">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sites</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">size</span><span class="o" style="font-weight: 600;">()-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--){</span></span>
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1350
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<td class="new_line diff-line-num old" data-linenumber="1350" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1350" 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;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sites</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;">i</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">slowScore</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">){</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sites</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);}</span></span>
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1350
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1350" 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;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sites</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;">i</span><span class="o" style="font-weight: 600;">).</span><span class="na" style="color: #008080;">slowScore</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">min</span><span class="o" style="font-weight: 600;">){</span><span class="c1" style="color: #998; font-style: italic;">//Fixed: max -> min, score -> slowscore</span></span>
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1351
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1351" class="line" lang="java"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">sites</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">remove</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1352" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1353" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1354" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(false) : r.mapScore+", "+max+", "+cap+", "+r.list;</span></span>
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1355
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1355" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(r.list.size()<2) : "\n"+max+", "+min+", "+r.list+"\n";</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/d4520373ab54d86278cb3713e4addaba8d2d8f0d#ef3b3e694c0bbaa70bf4c35a23c328ce44020fb6"><strong>current/shared/Shared.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="125" 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">@@ -125,8 +125,8 @@ public class Shared {</td>
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125
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125
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC125" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="no" style="color: #008080;">GAPCOST</span><span class="o" style="font-weight: 600;">=</span><span class="nc" style="color: #458; font-weight: 600;">Tools</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">max</span><span class="o" style="font-weight: 600;">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">,</span> <span class="no" style="color: #008080;">GAPLEN</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">64</span><span class="o" style="font-weight: 600;">);</span></span>
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126
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126
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC126" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">byte</span> <span class="no" style="color: #008080;">GAPC</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'-'</span><span class="o" style="font-weight: 600;">;</span></span>
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127
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127
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC127" class="line" lang="java"> </span>
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128
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC128" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">BBMAP_VERSION_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"38.9<span class="idiff left right deletion">5</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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129
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<td class="new_line diff-line-num old" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC129" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">BBMAP_VERSION_NAME</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right deletion">CFS Migration</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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128
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC128" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">BBMAP_VERSION_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"38.9<span class="idiff left right addition">6</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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129
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC129" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">BBMAP_VERSION_NAME</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right addition">Return True</span>"</span><span class="o" style="font-weight: 600;">;</span></span>
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130
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130
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC130" class="line" lang="java"> </span>
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131
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131
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC131" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="no" style="color: #008080;">TRIM_READ_COMMENTS</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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132
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132
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC132" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">boolean</span> <span class="no" style="color: #008080;">TRIM_RNAME</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">false</span><span class="o" style="font-weight: 600;">;</span> <span class="c1" style="color: #998; font-style: italic;">//For mapped sam reads</span></span>
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<a href="https://salsa.debian.org/med-team/bbmap/-/commit/d4520373ab54d86278cb3713e4addaba8d2d8f0d#4e3d7fe28dc46e7f8ac37caf3057c12574899ec3"><strong>current/stream/ReadStreamByteWriter.java</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="574" 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="574" 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">@@ -574,6 +574,8 @@ public class ReadStreamByteWriter extends ReadStreamWriter {</td>
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574
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574
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC574" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">SamLine</span> <span class="n" style="color: #333;">sl1</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">USE_ATTACHED_SAMLINE</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samline</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samline</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;">SamLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r</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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575
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575
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC575" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">SamLine</span> <span class="n" style="color: #333;">sl2</span><span class="o" style="font-weight: 600;">=(</span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">USE_ATTACHED_SAMLINE</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samline</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">null</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">samline</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;">SamLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">)));</span></span>
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576
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576
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC576" class="line" lang="java"></span>
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577
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC577" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(false) : OUTPUT_SAM_SECONDARY_ALIGNMENTS+", "+r.numSites()+", "+r.sites;</span></span>
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578
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC578" class="line" lang="java"> </span>
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577
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579
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC579" 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;">r</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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580
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC580" class="line" lang="java"> </span>
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579
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581
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC581" 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;">verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">numSites</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 unfold js-unfold old_line" data-linenumber="640" 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="642" 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">@@ -640,7 +642,7 @@ public class ReadStreamByteWriter extends ReadStreamWriter {</td>
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640
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642
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC642" class="line" lang="java"> <span class="n" style="color: #333;">clone</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setFromSite</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">ss</span><span class="o" style="font-weight: 600;">);</span></span>
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641
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643
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC643" class="line" lang="java"> <span class="n" style="color: #333;">clone</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">setSecondary</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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642
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644
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC644" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// assert(false) : r.mapScore+"\n"+ss.header()+"\n"+r.list+"\n";</span></span>
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643
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC643" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">SamLine</span> <span class="n" style="color: #333;">sl</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;">SamLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">clone</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;"><span class="idiff left right deletion">0</span></span><span class="o" style="font-weight: 600;">);</span></span>
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645
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC645" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">SamLine</span> <span class="n" style="color: #333;">sl</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;">SamLine</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">clone</span><span class="o" style="font-weight: 600;">,</span> <span class="mi" style="color: #099;"><span class="idiff left right addition">1</span></span><span class="o" style="font-weight: 600;">);</span></span>
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644
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646
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC646" class="line" lang="java"> <span class="k" style="font-weight: 600;">assert</span><span class="o" style="font-weight: 600;">(!</span><span class="n" style="color: #333;">sl</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">primary</span><span class="o" style="font-weight: 600;">());</span></span>
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645
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647
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC647" class="line" lang="java"><span class="c1" style="color: #998; font-style: italic;">// sl.setPrimary(false);</span></span>
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648
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC648" class="line" lang="java"> </span>
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