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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/kallisto">Debian Med / kallisto</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/fc9b521a1cceb845cda67a025962923e00578ff8">fc9b521a</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-08T22:14:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.46.1+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/fe424b28f21cdb086659db6ee1e564ca0b6b6b4f">fe424b28</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-08T22:14:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/f956fe50b29e4e18dc423ac9f46377c49e2ad12d">f956fe50</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-08T22:14:33Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.46.1+dfsg'
Update to upstream version '0.46.1+dfsg'
with Debian dir 10d91ad10e14c2dd5b87af938cb9604bfeaa1229</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/commit/79ce01c1e7c21ef09950fa0c79e02cac2c6abcca">79ce01c1</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-08T22:20:49Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version.
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#04f5818132a24af33b4b06c29540101bbc992c0b">
src/ProcessReads.cpp
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<li class="file-stats">
<a href="#c9d576083b226885d32fcec0ac23456a74eb4060">
src/ProcessReads.h
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<li class="file-stats">
<a href="#742351309009b70e28c04c50b75d5287975926bb">
src/common.h
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<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/kallisto/compare/be9e6cf5d8ad9f0c90b203b70c88d5c92793871f...79ce01c1e7c21ef09950fa0c79e02cac2c6abcca#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" 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">@@ -18,3 +18,6 @@ CTestTestfile.cmake</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">debug/</span>
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">release/</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">.vscode/</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">ext/htslib/src/htslib-stamp</span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">ext/htslib/tmp/</span>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.snakemake</span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/kallisto/compare/be9e6cf5d8ad9f0c90b203b70c88d5c92793871f...79ce01c1e7c21ef09950fa0c79e02cac2c6abcca#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -5,11 +5,11 @@ RNA-Seq data, or more generally of target sequences using high-throughput</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">sequencing reads. It is based on the novel idea of _pseudoalignment_ for</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown">rapidly determining the compatibility of reads with targets, without the need</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">for alignment. On benchmarks with standard RNA-Seq data, __kallisto__ can</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown">quantify 30 million human reads in less than 3 minutes on a Mac desktop</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">quantify 30 million human <span class="idiff left right">bulk RNA-seq </span>reads in less than 3 minutes on a Mac desktop</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown">computer using only the read sequences and a transcriptome index that</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown">itself takes <span class="idiff left right">less </span>than 10 minutes to build. Pseudoalignment of reads</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">itself takes than 10 minutes to build. Pseudoalignment of reads</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown">preserves the key information needed for quantification, and __kallisto__</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">is therefore not only fast, but also <span class="idiff left right">as accurate than</span> existing</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">is therefore not only fast, but also <span class="idiff left right">comparably accurate to other</span> existing</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown">quantification tools. In fact, because the pseudoalignment procedure is</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">robust to errors in the reads, in many benchmarks __kallisto__</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown">significantly outperforms existing tools. The __kallisto__ algorithms are described in more detail in:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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">@@ -18,7 +18,9 @@ NL Bray, H Pimentel, P Melsted and L Pachter, [Near optimal probabilistic RNA-se</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">Scripts reproducing all the results of the paper are available <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/pachterlab/kallisto_paper_analysis</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__kallisto__</span> quantified RNA-Seq can be analyzed with <span class="p">[</span><span class="nv" style="color: #008080;">__sleuth__</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/pachterlab/sleuth/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__kallisto__</span> quantified bulk RNA-Seq can be analyzed with <span class="p">[</span><span class="nv" style="color: #008080;">__sleuth__</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/pachterlab/sleuth/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__kallisto__</span> can be used together with <span class="p">[</span><span class="nv" style="color: #008080;">__bustools__</span><span class="p">](</span><span class="sx" style="color: #d14;">https://bustools.github.io/</span><span class="p">)</span> to pre-process single-cell RNA-seq data. See the <span class="p">[</span><span class="nv" style="color: #008080;">kallistobus.tools</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.kallistobus.tools/</span><span class="p">)</span> website for instructions.</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Manual</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" 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="28" 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">@@ -26,24 +28,15 @@ Please visit http://pachterlab.github.io/kallisto/manual.html for the manual.</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## License</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown">Please read the license before using kallisto. The license is distributed with __kallisto__ in the file <span class="sb" style="color: #d14;">`license.txt`</span> also viewable <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://pachterlab.github.io/kallisto/download</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Announcements</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown">There is a low traffic Google Group,</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">kallisto-sleuth-announcements</span><span class="p">](</span><span class="sx" style="color: #d14;">https://groups.google.com/d/forum/kallisto-sleuth-announcements</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown">where we make announcements about new releases. This is a read-only mailing</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown">list.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__kallisto__</span> is distributed under the BSD-2 license. The license is distributed with __kallisto__ in the file <span class="sb" style="color: #d14;">`license.txt`</span>, which is also viewable <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://pachterlab.github.io/kallisto/download</span><span class="p">)</span>. Please read the license before using __kallisto__.</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Getting help</span></span>
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown">For help running __kallisto__, please post to the <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>kallisto-sleuth-users</span>
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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown">Google Group](https://groups.google.com/d/forum/kallisto-sleuth-users).</span>
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<td class="diff-line-num new new_line" data-linenumber="35" 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">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">For help running __kallisto__, please post to the <span class="p">[</span><span class="nv" style="color: #008080;">kallisto-and-applications Google Group</span><span class="p">](</span><span class="sx" style="color: #d14;">https://groups.google.com/forum/#!forum/kallisto-and-applications</span><span class="p">)</span>.</span>
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42
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>
</pre>
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43
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Reporting bugs</span></span>
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44
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown">Please report bugs to the <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>Github issues</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown">page](https://github.com/pachterlab/kallisto/issues)</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown">Please report bugs to the <span class="p">[</span><span class="nv" style="color: #008080;">Github issues page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/pachterlab/kallisto/issues</span><span class="p">)</span></span>
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47
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Development and pull requests</span></span>
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49
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"></span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kallisto/compare/be9e6cf5d8ad9f0c90b203b70c88d5c92793871f...79ce01c1e7c21ef09950fa0c79e02cac2c6abcca#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kallisto (0.46.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Fri, 08 Nov 2019 23:14:36 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">kallisto (0.46.0+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/kallisto/compare/be9e6cf5d8ad9f0c90b203b70c88d5c92793871f...79ce01c1e7c21ef09950fa0c79e02cac2c6abcca#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libhdf5-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libhts-dev</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/kallisto</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/kallisto.git</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://pachterlab.github.io/kallisto</span>
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<a href="https://salsa.debian.org/med-team/kallisto/compare/be9e6cf5d8ad9f0c90b203b70c88d5c92793871f...79ce01c1e7c21ef09950fa0c79e02cac2c6abcca#04f5818132a24af33b4b06c29540101bbc992c0b"><strong>src/ProcessReads.cpp</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">@@ -256,7 +256,7 @@ int64_t ProcessBUSReads(MasterProcessor& MP, const ProgramOptions& opt) {</td>
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nummapped</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[~warn] no reads pseudoaligned."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">numreads</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"></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">@@ -565,7 +565,7 @@ void MasterProcessor::processAln(const EMAlgorithm& em, bool useEM = true) {</td>
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565
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"></span>
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566
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">pseudobam</span><span class="p">);</span></span>
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567
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp"> <span class="n" style="color: #333;">pseudobatchf_in</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/pseudoaln.bin"</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="cpp"> <span class="n" style="color: #333;">SR</span><span class="p"><span class="idiff left right">.</span></span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="n" style="color: #333;">SR</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-></span></span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="cpp"></span>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">workers</span><span class="p">;</span></span>
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571
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="893" 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">@@ -893,6 +893,7 @@ ReadProcessor::ReadProcessor(ReadProcessor && o) :</td>
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893
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893
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="cpp"> <span class="n" style="color: #333;">seqs</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">seqs</span><span class="p">)),</span></span>
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894
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="cpp"> <span class="n" style="color: #333;">names</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">names</span><span class="p">)),</span></span>
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895
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="cpp"> <span class="n" style="color: #333;">quals</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">quals</span><span class="p">)),</span></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="cpp"> <span class="n" style="color: #333;">flags</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">flags</span><span class="p">)),</span></span>
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897
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<pre style="margin: 0;"> <span id="LC897" class="line" lang="cpp"> <span class="n" style="color: #333;">umis</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">umis</span><span class="p">)),</span></span>
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="cpp"> <span class="n" style="color: #333;">newEcs</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">newEcs</span><span class="p">)),</span></span>
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="cpp"> <span class="n" style="color: #333;">flens</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">flens</span><span class="p">)),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="919" 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="920" 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">@@ -919,16 +920,16 @@ void ReadProcessor::operator()() {</td>
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919
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920
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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920
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921
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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921
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922
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="922" 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">
922
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="n" style="color: #333;">bufsize</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">pseudobam</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="n" style="color: #333;">bufsize</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">pseudobam</span> <span class="p">);</span></span>
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923
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924
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="cpp"> <span class="p">}</span></span>
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924
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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925
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926
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lock_guard</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">reader_lock</span><span class="p">);</span></span>
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926
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<td class="diff-line-num new_line old" data-linenumber="927" 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="LC926" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="p"><span class="idiff left right">.</span></span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-></span></span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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927
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// nothing to do</span></span>
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928
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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929
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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930
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// get new sequences</span></span>
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931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="cpp"> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">fetchSequences</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bufsize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seqs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">qual</span>s</span><span class="p">,</span> <span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">pseudobam</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fusion</span><span class="p">);</span></span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="o" style="font-weight: 600;"><span class="idiff left">-></span></span><span class="n" style="color: #333;"><span class="idiff">fetchSequences</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bufsize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seqs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">flag</span>s</span><span class="p">,</span> <span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">pseudobam</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fusion</span><span class="p">);</span></span>
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932
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="cpp"> <span class="p">}</span></span>
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933
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// release the reader lock</span></span>
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934
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1222" 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">@@ -1222,7 +1223,7 @@ void ReadProcessor::clear() {</td>
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1223
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<pre style="margin: 0;"> <span id="LC1223" class="line" lang="cpp"></span>
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1223
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1224
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<pre style="margin: 0;"> <span id="LC1224" class="line" lang="cpp"></span>
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1224
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1225
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<pre style="margin: 0;"> <span id="LC1225" class="line" lang="cpp"><span class="n" style="color: #333;">BUSProcessor</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BUSProcessor</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">KmerIndex</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">MinCollector</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tc</span><span class="p">,</span> <span class="n" style="color: #333;">MasterProcessor</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_id</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">_local_id</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC1225" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">single_end</span><span class="p">),</span> <span class="n" style="color: #333;">tc</span><span class="p">(</span><span class="n" style="color: #333;">tc</span><span class="p">),</span> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">mp</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">),</span> <span class="n" style="color: #333;">id</span><span class="p">(</span><span class="n" style="color: #333;">_id</span><span class="p">),</span> <span class="n" style="color: #333;">local_id</span><span class="p">(</span><span class="n" style="color: #333;">_local_id</span><span class="p">)</span> <span class="p">{</span></span>
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1226
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">single_end</span><span class="p">),</span> <span class="n" style="color: #333;"><span class="idiff left">bam</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bam</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">num</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">num</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">tc</span><span class="p">(</span><span class="n" style="color: #333;">tc</span><span class="p">),</span> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">mp</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">),</span> <span class="n" style="color: #333;">id</span><span class="p">(</span><span class="n" style="color: #333;">_id</span><span class="p">),</span> <span class="n" style="color: #333;">local_id</span><span class="p">(</span><span class="n" style="color: #333;">_local_id</span><span class="p">)</span> <span class="p">{</span></span>
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1226
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<td class="diff-line-num new_line" data-linenumber="1227" 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">
1227
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<pre style="margin: 0;"> <span id="LC1227" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// initialize buffer</span></span>
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1227
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1228
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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="cpp"> <span class="n" style="color: #333;">bufsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">bufsize</span><span class="p">;</span></span>
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1228
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1229
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<pre style="margin: 0;"> <span id="LC1229" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">bufsize</span><span class="p">];</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1238" 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="1239" 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">@@ -1238,6 +1239,8 @@ BUSProcessor::BUSProcessor(const KmerIndex& index, const ProgramOptions& opt, co</td>
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1238
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1239
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<pre style="margin: 0;"> <span id="LC1239" class="line" lang="cpp"></span>
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1239
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1240
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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="cpp"><span class="n" style="color: #333;">BUSProcessor</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BUSProcessor</span><span class="p">(</span><span class="n" style="color: #333;">BUSProcessor</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">o</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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1240
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1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">paired</span><span class="p">),</span></span>
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1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="cpp"> <span class="n" style="color: #333;">bam</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">),</span></span>
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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="cpp"> <span class="n" style="color: #333;">num</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">num</span><span class="p">),</span></span>
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1241
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1244
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="cpp"> <span class="n" style="color: #333;">tc</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">tc</span><span class="p">),</span></span>
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1242
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1245
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">),</span></span>
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1243
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1246
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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="cpp"> <span class="n" style="color: #333;">mp</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">mp</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1248" 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="1251" 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">@@ -1248,6 +1251,7 @@ BUSProcessor::BUSProcessor(BUSProcessor && o) :</td>
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1248
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1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="cpp"> <span class="n" style="color: #333;">seqs</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">seqs</span><span class="p">)),</span> </span>
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1249
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1252
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<pre style="margin: 0;"> <span id="LC1252" class="line" lang="cpp"> <span class="n" style="color: #333;">names</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">names</span><span class="p">)),</span></span>
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1250
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1253
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<pre style="margin: 0;"> <span id="LC1253" class="line" lang="cpp"> <span class="n" style="color: #333;">quals</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">quals</span><span class="p">)),</span></span>
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1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="cpp"> <span class="n" style="color: #333;">flags</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">flags</span><span class="p">)),</span></span>
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1255
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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="cpp"> <span class="n" style="color: #333;">newEcs</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">newEcs</span><span class="p">)),</span></span>
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1256
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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="cpp"> <span class="n" style="color: #333;">flens</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">flens</span><span class="p">)),</span></span>
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1257
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<pre style="margin: 0;"> <span id="LC1257" class="line" lang="cpp"> <span class="n" style="color: #333;">bias5</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">bias5</span><span class="p">)),</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">@@ -1273,13 +1277,13 @@ void BUSProcessor::operator()() {</td>
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1273
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1277
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// grab the reader lock</span></span>
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1274
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="p">{</span></span>
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1275
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lock_guard</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">reader_lock</span><span class="p">);</span></span>
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1276
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<pre style="margin: 0;">-<span id="LC1276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="p"><span class="idiff left right">.</span></span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-></span></span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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1277
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1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// nothing to do</span></span>
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1278
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1282
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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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1279
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1283
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1284
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// get new sequences</span></span>
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1281
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1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">umis</span><span class="p">;</span></span>
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1282
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<pre style="margin: 0;">-<span id="LC1282" class="line" lang="cpp"> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">fetchSequences</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bufsize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seqs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">qual</span>s</span><span class="p">,</span> <span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp"> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="o" style="font-weight: 600;"><span class="idiff left">-></span></span><span class="n" style="color: #333;"><span class="idiff">fetchSequences</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bufsize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seqs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">flag</span>s</span><span class="p">,</span> <span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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1287
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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="cpp"> <span class="p">}</span></span>
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1288
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<pre style="margin: 0;"> <span id="LC1288" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// release the reader lock</span></span>
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1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1304" 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="1308" 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">@@ -1304,7 +1308,7 @@ void BUSProcessor::processBuffer() {</td>
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1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">KmerEntry</span><span class="p">,</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;">v</span><span class="p">,</span><span class="n" style="color: #333;">v2</span><span class="p">;</span></span>
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1305
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1309
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<pre style="margin: 0;"> <span id="LC1309" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">vtmp</span><span class="p">;</span></span>
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1306
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1310
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<pre style="margin: 0;"> <span id="LC1310" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">u</span><span class="p">;</span></span>
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1307
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<pre style="margin: 0;">-<span id="LC1307" class="line" lang="cpp"></span>
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1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="cpp"> </span>
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1308
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1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="cpp"> <span class="n" style="color: #333;">u</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">);</span></span>
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1309
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1313
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="cpp"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">);</span></span>
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1310
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1314
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<pre style="margin: 0;"> <span id="LC1314" class="line" lang="cpp"> <span class="n" style="color: #333;">vtmp</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">);</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">@@ -1326,9 +1330,17 @@ void BUSProcessor::processBuffer() {</td>
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1326
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1330
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="cpp"> </span>
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1327
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1331
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// actually process the sequences</span></span>
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1328
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1332
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BUSOptions</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">busopt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">busOptions</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1329" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">incf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">incf</span><span class="p">,</span> <span class="n" style="color: #333;">jmax</span><span class="p">;</span></span>
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1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">)</span> <span class="p">{</span></span>
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1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="cpp"> <span class="n" style="color: #333;">incf</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="cpp"> <span class="n" style="color: #333;">jmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="cpp"> <span class="n" style="color: #333;">incf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="cpp"> <span class="n" style="color: #333;">jmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="cpp"> <span class="p">}</span></span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//int incf = (bam) ? 1 : busopt.nfiles-1;</span></span>
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1330
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<td class="diff-line-num new_line" data-linenumber="1342" 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">
1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">incf</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1331
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<td class="diff-line-num new_line old" data-linenumber="1343" 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="LC1331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">busopt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nfiles</span></span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1343" 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">
1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">jmax</span></span><span class="idiff"> </span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/*(bam) ? 2 : busopt.nfiles*/</span></span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1332
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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1333
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1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="cpp"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span> </span>
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<td class="diff-line-num old_line" data-linenumber="1334" 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">
1334
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1346
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<pre style="margin: 0;"> <span id="LC1346" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1350" 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="1362" 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">@@ -1350,7 +1362,7 @@ void BUSProcessor::processBuffer() {</td>
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1350
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1362
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<pre style="margin: 0;"> <span id="LC1362" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1351" 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">
1351
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1363
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<pre style="margin: 0;"> <span id="LC1363" class="line" lang="cpp"></span>
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1352
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1364
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="cpp"> </span>
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<td class="diff-line-num old old_line" data-linenumber="1353" 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">
1353
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<td class="diff-line-num new_line old" data-linenumber="1365" 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="LC1353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bcc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span> auto &bcc = busopt.bc[0];</span></span>
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1354
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<td class="diff-line-num new_line" data-linenumber="1366" 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">
1366
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<pre style="margin: 0;"> <span id="LC1366" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1355" 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">
1355
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<td class="diff-line-num new_line" data-linenumber="1367" 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">
1367
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<pre style="margin: 0;"> <span id="LC1367" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">bad_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1356
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1368
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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bcc</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1401" 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="1413" 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">@@ -1401,6 +1413,9 @@ void BUSProcessor::processBuffer() {</td>
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1401
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<td class="diff-line-num new_line" data-linenumber="1413" 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">
1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">|=</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1402" 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">
1402
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<td class="diff-line-num new_line" data-linenumber="1414" 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">
1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1403" 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">
1403
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<td class="diff-line-num new_line" data-linenumber="1415" 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">
1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//std::cout << std::string(s1,10) << "\t" << b.barcode << "\t" << std::string(s1+10,16) << "\t" << b.UMI << "\n";</span></span>
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1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1417" 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">
1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">flags</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">jmax</span><span class="p">];</span></span>
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1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="cpp"> <span class="p">}</span></span>
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1404
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1419
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1405" 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">
1405
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1420
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<pre style="margin: 0;"> <span id="LC1420" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//ec = tc.findEC(u);</span></span>
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1406
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<td class="diff-line-num new_line" data-linenumber="1421" 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">
1421
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<pre style="margin: 0;"> <span id="LC1421" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1438" 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="1453" 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">@@ -1438,8 +1453,7 @@ AlnProcessor::AlnProcessor(const KmerIndex& index, const ProgramOptions& opt, Ma</td>
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1438
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<td class="diff-line-num new_line" data-linenumber="1453" 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">
1453
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<pre style="margin: 0;"> <span id="LC1453" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">bufsize</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="1439" 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">
1439
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<td class="diff-line-num new_line" data-linenumber="1454" 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">
1454
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<pre style="margin: 0;"> <span id="LC1454" class="line" lang="cpp"> <span class="n" style="color: #333;">bambufsize</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="mi" style="color: #099;">20</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1440" 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">
1440
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<td class="diff-line-num new_line" data-linenumber="1455" 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">
1455
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<pre style="margin: 0;"> <span id="LC1455" class="line" lang="cpp"> <span class="n" style="color: #333;">bambuffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">[</span><span class="n" style="color: #333;">bambufsize</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// refactor this?</span></span>
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1441
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<pre style="margin: 0;">-<span id="LC1441" class="line" lang="cpp"></span>
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1442
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<pre style="margin: 0;">-<span id="LC1442" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="1443" 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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1456
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<pre style="margin: 0;">+<span id="LC1456" class="line" lang="cpp"> </span>
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1443
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<td class="diff-line-num new_line" data-linenumber="1457" 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">
1457
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<pre style="margin: 0;"> <span id="LC1457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_mode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1444" 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">
1444
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<td class="diff-line-num new_line" data-linenumber="1458" 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">
1458
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<pre style="margin: 0;"> <span id="LC1458" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* need to check this later */</span></span>
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<td class="diff-line-num old_line" data-linenumber="1445" 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">
1445
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1459
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<pre style="margin: 0;"> <span id="LC1459" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">id</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="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1475" 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="1489" 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">@@ -1475,6 +1489,7 @@ AlnProcessor::AlnProcessor(AlnProcessor && o) :</td>
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<td class="diff-line-num old_line" data-linenumber="1475" 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">
1475
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1489
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<pre style="margin: 0;"> <span id="LC1489" class="line" lang="cpp"> <span class="n" style="color: #333;">seqs</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">seqs</span><span class="p">)),</span></span>
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<td class="diff-line-num old_line" data-linenumber="1476" 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">
1476
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<td class="diff-line-num new_line" data-linenumber="1490" 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">
1490
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<pre style="margin: 0;"> <span id="LC1490" class="line" lang="cpp"> <span class="n" style="color: #333;">names</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">names</span><span class="p">)),</span></span>
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<td class="diff-line-num old_line" data-linenumber="1477" 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">
1477
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<td class="diff-line-num new_line" data-linenumber="1491" 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">
1491
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<pre style="margin: 0;"> <span id="LC1491" class="line" lang="cpp"> <span class="n" style="color: #333;">quals</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">quals</span><span class="p">)),</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1478" 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="1492" 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">
1492
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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="cpp"> <span class="n" style="color: #333;">flags</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">flags</span><span class="p">)),</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1478" 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">
1478
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<td class="diff-line-num new_line" data-linenumber="1493" 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">
1493
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<pre style="margin: 0;"> <span id="LC1493" class="line" lang="cpp"> <span class="n" style="color: #333;">umis</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">umis</span><span class="p">)),</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1479" 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">
1479
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<td class="diff-line-num new_line" data-linenumber="1494" 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">
1494
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<pre style="margin: 0;"> <span id="LC1494" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">batchSR</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1480" 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">
1480
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<td class="diff-line-num new_line" data-linenumber="1495" 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">
1495
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<pre style="margin: 0;"> <span id="LC1495" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">buffer</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1515" 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="1530" 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">@@ -1515,19 +1530,19 @@ void AlnProcessor::operator()() {</td>
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<td class="diff-line-num old_line" data-linenumber="1515" 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">
1515
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<td class="diff-line-num new_line" data-linenumber="1530" 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">
1530
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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1516" 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">
1516
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<td class="diff-line-num new_line" data-linenumber="1531" 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">
1531
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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1517" 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">
1517
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<td class="diff-line-num new_line" data-linenumber="1532" 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">
1532
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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1518" 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">
1518
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<td class="diff-line-num new_line old" data-linenumber="1533" 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="LC1518" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="n" style="color: #333;">bufsize</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span> <span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1519" 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="1533" 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">
1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="n" style="color: #333;">bufsize</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">flags</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span> <span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1519" 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">
1519
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<td class="diff-line-num new_line" data-linenumber="1534" 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">
1534
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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="cpp"> <span class="n" style="color: #333;">readPseudoAlignmentBatch</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">pseudobatchf_in</span><span class="p">,</span> <span class="n" style="color: #333;">pseudobatch</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1520" 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">
1520
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<td class="diff-line-num new_line" data-linenumber="1535" 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">
1535
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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pseudobatch</span><span class="p">.</span><span class="n" style="color: #333;">batch_id</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1521" 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">
1521
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<td class="diff-line-num new_line" data-linenumber="1536" 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">
1536
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<pre style="margin: 0;"> <span id="LC1536" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pseudobatch</span><span class="p">.</span><span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">((</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()));</span> <span class="c1" style="color: #998; font-style: italic;">// sanity checks</span></span>
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<td class="diff-line-num old_line" data-linenumber="1522" 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">
1522
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<td class="diff-line-num new_line" data-linenumber="1537" 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">
1537
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<pre style="margin: 0;"> <span id="LC1537" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1523" 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">
1523
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<td class="diff-line-num new_line" data-linenumber="1538" 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">
1538
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<pre style="margin: 0;"> <span id="LC1538" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1524" 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">
1524
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<td class="diff-line-num new_line" data-linenumber="1539" 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">
1539
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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lock_guard</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">reader_lock</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1525" 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">
1525
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<td class="diff-line-num new_line old" data-linenumber="1540" 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="LC1525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="p"><span class="idiff left right">.</span></span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1526" 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="1540" 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">
1540
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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-></span></span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1526" 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">
1526
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<td class="diff-line-num new_line" data-linenumber="1541" 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">
1541
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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// nothing to do</span></span>
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<td class="diff-line-num old_line" data-linenumber="1527" 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">
1527
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<td class="diff-line-num new_line" data-linenumber="1542" 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">
1542
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1528" 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">
1528
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<td class="diff-line-num new_line" data-linenumber="1543" 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">
1543
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1529" 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">
1529
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<td class="diff-line-num new_line" data-linenumber="1544" 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">
1544
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<pre style="margin: 0;"> <span id="LC1544" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// get new sequences </span></span>
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1530
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<pre style="margin: 0;">-<span id="LC1530" class="line" lang="cpp"> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">fetchSequences</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bufsize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seqs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">qual</span>s</span><span class="p">,</span> <span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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1545
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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="cpp"> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">SR</span><span class="o" style="font-weight: 600;"><span class="idiff left">-></span></span><span class="n" style="color: #333;"><span class="idiff">fetchSequences</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bufsize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">seqs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">quals</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">flag</span>s</span><span class="p">,</span> <span class="n" style="color: #333;">umis</span><span class="p">,</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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1531
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1546
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<pre style="margin: 0;"> <span id="LC1546" class="line" lang="cpp"> <span class="n" style="color: #333;">readPseudoAlignmentBatch</span><span class="p">(</span><span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">pseudobatchf_in</span><span class="p">,</span> <span class="n" style="color: #333;">pseudobatch</span><span class="p">);</span></span>
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1532
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1547
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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pseudobatch</span><span class="p">.</span><span class="n" style="color: #333;">batch_id</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">);</span></span>
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1533
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1548
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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pseudobatch</span><span class="p">.</span><span class="n" style="color: #333;">aln</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">((</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()));</span> <span class="c1" style="color: #998; font-style: italic;">// sanity checks</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">@@ -2557,9 +2572,14 @@ int fillBamRecord(bam1_t &b, uint8_t* buf, const char *seq, const char *name, co</td>
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<pre style="margin: 0;"> <span id="LC2572" class="line" lang="cpp"><span class="p">}</span></span>
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2573
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<pre style="margin: 0;"> <span id="LC2573" class="line" lang="cpp"></span>
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2574
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<pre style="margin: 0;"> <span id="LC2574" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2560" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** -- sequence reader -- **/</span></span>
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<pre style="margin: 0;">+<span id="LC2575" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** -- sequence readers -- **/</span></span>
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2576
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<pre style="margin: 0;">+<span id="LC2576" class="line" lang="cpp"></span>
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2577
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<pre style="margin: 0;">+<span id="LC2577" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reset</span><span class="p">()</span> <span class="p">{</span></span>
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2578
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<pre style="margin: 0;">+<span id="LC2578" class="line" lang="cpp"> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2579
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<pre style="margin: 0;">+<span id="LC2579" class="line" lang="cpp"> <span class="n" style="color: #333;">readbatch_id</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="p">;</span></span>
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2580
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<pre style="margin: 0;">+<span id="LC2580" class="line" lang="cpp"><span class="p">}</span></span>
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2561
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2581
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<pre style="margin: 0;"> <span id="LC2581" class="line" lang="cpp"></span>
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2562
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<pre style="margin: 0;">-<span id="LC2562" class="line" lang="cpp"><span class="n" style="color: #333;"><span class="idiff left">SequenceReader</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::~</span></span><span class="n" style="color: #333;">SequenceReader</span><span class="p">()</span> <span class="p">{</span></span>
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2582
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<pre style="margin: 0;">+<span id="LC2582" class="line" lang="cpp"><span class="n" style="color: #333;"><span class="idiff left">FastqSequenceReader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::~</span></span><span class="n" style="color: #333;"><span class="idiff right">Fastq</span>SequenceReader</span><span class="p">()</span> <span class="p">{</span></span>
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2563
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2583
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<pre style="margin: 0;"> <span id="LC2583" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="p">{</span></span>
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2584
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<pre style="margin: 0;"> <span id="LC2584" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>
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2585
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<pre style="margin: 0;"> <span id="LC2585" class="line" lang="cpp"> <span class="n" style="color: #333;">gzclose</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</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">@@ -2578,26 +2598,20 @@ SequenceReader::~SequenceReader() {</td>
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2598
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<pre style="margin: 0;"> <span id="LC2598" class="line" lang="cpp"><span class="p">}</span></span>
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2599
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<pre style="margin: 0;"> <span id="LC2599" class="line" lang="cpp"></span>
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2600
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<pre style="margin: 0;"> <span id="LC2600" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2581" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reserveNfiles</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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2582
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<pre style="margin: 0;">-<span id="LC2582" class="line" lang="cpp"> <span class="n" style="color: #333;">fp</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2583" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">);</span></span>
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2584
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<pre style="margin: 0;">-<span id="LC2584" class="line" lang="cpp"> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2585
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<pre style="margin: 0;">-<span id="LC2585" class="line" lang="cpp"> <span class="n" style="color: #333;">nl</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2601" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">FastqSequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2602" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">current_file</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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2603
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<pre style="margin: 0;"> <span id="LC2603" class="line" lang="cpp"><span class="p">}</span></span>
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2604
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<pre style="margin: 0;"> <span id="LC2604" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2588" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reset</span><span class="p">()</span> <span class="p">{</span></span>
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2589
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<pre style="margin: 0;">-<span id="LC2589" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2605" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">FastqSequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reset</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2606" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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2607
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<pre style="margin: 0;">+<span id="LC2607" class="line" lang="cpp"> </span>
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2608
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<pre style="margin: 0;">+<span id="LC2608" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="p">{</span></span>
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2590
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2609
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<pre style="margin: 0;"> <span id="LC2609" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>
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2591
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2610
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<pre style="margin: 0;"> <span id="LC2610" class="line" lang="cpp"> <span class="n" style="color: #333;">gzclose</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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2592
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2611
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<pre style="margin: 0;"> <span id="LC2611" class="line" lang="cpp"> <span class="p">}</span></span>
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2593
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2612
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<pre style="margin: 0;"> <span id="LC2612" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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2594
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2613
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<pre style="margin: 0;"> <span id="LC2613" class="line" lang="cpp"> <span class="p">}</span></span>
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2595
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<td class="diff-line-num new_line" data-linenumber="2614" 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">
2614
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<pre style="margin: 0;"> <span id="LC2614" class="line" lang="cpp"></span>
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2596
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<pre style="margin: 0;">-<span id="LC2596" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2597" 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">
2597
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<td class="diff-line-num new_line old" data-linenumber="2615" 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="LC2597" class="line" lang="cpp"> <span class="n" style="color: #333;">kseq_destroy</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2598" 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">
2598
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<td class="diff-line-num new_line old" data-linenumber="2615" 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="LC2598" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2599" 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">
2599
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<pre style="margin: 0;">-<span id="LC2599" class="line" lang="cpp"> <span class="p">}</span></span>
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2600
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<pre style="margin: 0;">-<span id="LC2600" class="line" lang="cpp"></span>
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2601
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2615
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<pre style="margin: 0;"> <span id="LC2615" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_umi</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_umi</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>
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2602
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2616
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<pre style="margin: 0;"> <span id="LC2616" class="line" lang="cpp"> <span class="n" style="color: #333;">f_umi</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">close</span><span class="p">();</span> </span>
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2603
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2617
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<pre style="margin: 0;"> <span id="LC2617" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2612" 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="2626" 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">@@ -2612,15 +2626,24 @@ void SequenceReader::reset() {</td>
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2612
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2626
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<pre style="margin: 0;"> <span id="LC2626" class="line" lang="cpp"> <span class="p">}</span></span>
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2613
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2627
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<pre style="margin: 0;"> <span id="LC2627" class="line" lang="cpp"> </span>
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2614
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<td class="diff-line-num new_line" data-linenumber="2628" 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">
2628
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<pre style="margin: 0;"> <span id="LC2628" class="line" lang="cpp"> <span class="n" style="color: #333;">current_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2615
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<pre style="margin: 0;">-<span id="LC2615" class="line" lang="cpp"> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2616
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<pre style="margin: 0;">-<span id="LC2616" class="line" lang="cpp"> <span class="n" style="color: #333;">readbatch_id</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="p">;</span></span>
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2629
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<pre style="margin: 0;">+<span id="LC2629" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="p">{</span></span>
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2630
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<pre style="margin: 0;">+<span id="LC2630" class="line" lang="cpp"> <span class="n" style="color: #333;">kseq_destroy</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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2631
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<pre style="margin: 0;">+<span id="LC2631" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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2632
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<pre style="margin: 0;">+<span id="LC2632" class="line" lang="cpp"> <span class="p">}</span></span>
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2617
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2633
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<pre style="margin: 0;"> <span id="LC2633" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2634" class="line" lang="cpp"></span>
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2635
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<pre style="margin: 0;">+<span id="LC2635" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">FastqSequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reserveNfiles</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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2636
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<pre style="margin: 0;">+<span id="LC2636" class="line" lang="cpp"> <span class="n" style="color: #333;">fp</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">);</span></span>
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2637
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<pre style="margin: 0;">+<span id="LC2637" class="line" lang="cpp"> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2638
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<pre style="margin: 0;">+<span id="LC2638" class="line" lang="cpp"> <span class="n" style="color: #333;">nl</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2639
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<pre style="margin: 0;">+<span id="LC2639" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">);</span></span>
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2640
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<pre style="margin: 0;">+<span id="LC2640" class="line" lang="cpp"><span class="p">}</span></span>
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2619
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2641
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<pre style="margin: 0;"> <span id="LC2641" class="line" lang="cpp"></span>
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2620
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2642
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<pre style="margin: 0;"> <span id="LC2642" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// returns true if there is more left to read from the files</span></span>
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2621
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<pre style="margin: 0;">-<span id="LC2621" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limit</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span></span>
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2643
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<pre style="margin: 0;">+<span id="LC2643" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;"><span class="idiff left right">Fastq</span>SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limit</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span></span>
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2622
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2644
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<pre style="margin: 0;"> <span id="LC2644" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">names</span><span class="p">,</span></span>
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2623
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2645
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<pre style="margin: 0;"> <span id="LC2645" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">quals</span><span class="p">,</span></span>
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2646
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<pre style="margin: 0;">+<span id="LC2646" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">flags</span><span class="p">,</span></span>
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2624
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2647
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<pre style="margin: 0;"> <span id="LC2647" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">umis</span><span class="p">,</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;">read_id</span><span class="p">,</span></span>
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2625
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2648
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<pre style="margin: 0;"> <span id="LC2648" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">full</span><span class="p">)</span> <span class="p">{</span></span>
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2626
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2649
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<pre style="margin: 0;"> <span id="LC2649" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2634" 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="2657" 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">@@ -2634,6 +2657,7 @@ bool SequenceReader::fetchSequences(char *buf, const int limit, std::vector<std:</td>
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2634
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<td class="diff-line-num new_line" data-linenumber="2657" 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">
2657
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<pre style="margin: 0;"> <span id="LC2657" class="line" lang="cpp"> <span class="n" style="color: #333;">names</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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2635
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<td class="diff-line-num new_line" data-linenumber="2658" 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">
2658
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<pre style="margin: 0;"> <span id="LC2658" class="line" lang="cpp"> <span class="n" style="color: #333;">quals</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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2636
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<td class="diff-line-num new_line" data-linenumber="2659" 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">
2659
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<pre style="margin: 0;"> <span id="LC2659" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2637" 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="2660" 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">
2660
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<pre style="margin: 0;">+<span id="LC2660" class="line" lang="cpp"> <span class="n" style="color: #333;">flags</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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2637
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2661
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<pre style="margin: 0;"> <span id="LC2661" class="line" lang="cpp"> </span>
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<td class="diff-line-num old_line" data-linenumber="2638" 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">
2638
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<td class="diff-line-num new_line" data-linenumber="2662" 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">
2662
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<pre style="margin: 0;"> <span id="LC2662" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">usingUMIfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">umi_files</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="2639" 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">
2639
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<td class="diff-line-num new_line" data-linenumber="2663" 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">
2663
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<pre style="margin: 0;"> <span id="LC2663" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">umis_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2678" 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="2702" 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">@@ -2678,7 +2702,7 @@ bool SequenceReader::fetchSequences(char *buf, const int limit, std::vector<std:</td>
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<td class="diff-line-num old_line" data-linenumber="2678" 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">
2678
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<td class="diff-line-num new_line" data-linenumber="2702" 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">
2702
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<pre style="margin: 0;"> <span id="LC2702" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">all_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2679" 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">
2679
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<td class="diff-line-num new_line" data-linenumber="2703" 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">
2703
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<pre style="margin: 0;"> <span id="LC2703" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bufadd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nfiles</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2680" 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">
2680
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<td class="diff-line-num new_line" data-linenumber="2704" 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">
2704
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<pre style="margin: 0;"> <span id="LC2704" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nfiles</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2681" 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">
2681
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<td class="diff-line-num new_line old" data-linenumber="2705" 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="LC2681" class="line" lang="cpp"> <span class="n" style="color: #333;">all_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_l</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2682" 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="2705" 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">
2705
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<pre style="margin: 0;">+<span id="LC2705" class="line" lang="cpp"> <span class="n" style="color: #333;">all_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_l</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">><span class="idiff left right">=</span></span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2682" 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">
2682
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<td class="diff-line-num new_line" data-linenumber="2706" 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">
2706
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<pre style="margin: 0;"> <span id="LC2706" class="line" lang="cpp"> <span class="n" style="color: #333;">bufadd</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// includes seq</span></span>
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<td class="diff-line-num old_line" data-linenumber="2683" 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">
2683
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<td class="diff-line-num new_line" data-linenumber="2707" 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">
2707
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<pre style="margin: 0;"> <span id="LC2707" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2684" 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">
2684
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<td class="diff-line-num new_line" data-linenumber="2708" 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">
2708
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<pre style="margin: 0;"> <span id="LC2708" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">all_l</span><span class="p">)</span> <span class="p">{</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2718" 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="2742" 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">@@ -2718,6 +2742,8 @@ bool SequenceReader::fetchSequences(char *buf, const int limit, std::vector<std:</td>
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<td class="diff-line-num old_line" data-linenumber="2718" 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">
2718
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<td class="diff-line-num new_line" data-linenumber="2742" 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">
2742
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<pre style="margin: 0;"> <span id="LC2742" class="line" lang="cpp"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">umi</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2719" 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">
2719
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<td class="diff-line-num new_line" data-linenumber="2743" 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">
2743
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<pre style="margin: 0;"> <span id="LC2743" class="line" lang="cpp"> <span class="n" style="color: #333;">umis</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="2720" 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">
2720
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2744
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<pre style="margin: 0;"> <span id="LC2744" class="line" lang="cpp"> <span class="p">}</span></span>
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2745
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<pre style="margin: 0;">+<span id="LC2745" class="line" lang="cpp"></span>
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2746
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<pre style="margin: 0;">+<span id="LC2746" class="line" lang="cpp"> <span class="n" style="color: #333;">flags</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">numreads</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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2721
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2747
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<pre style="margin: 0;"> <span id="LC2747" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2722
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2748
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<pre style="margin: 0;"> <span id="LC2748" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// read it next time</span></span>
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2723
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2749
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<pre style="margin: 0;"> <span id="LC2749" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2732" 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">@@ -2732,27 +2758,146 @@ bool SequenceReader::fetchSequences(char *buf, const int limit, std::vector<std:</td>
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2732
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2758
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<pre style="margin: 0;"> <span id="LC2758" class="line" lang="cpp"> <span class="p">}</span></span>
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2733
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2759
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<pre style="margin: 0;"> <span id="LC2759" class="line" lang="cpp"><span class="p">}</span></span>
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2734
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2760
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<pre style="margin: 0;"> <span id="LC2760" class="line" lang="cpp"></span>
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2735
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<pre style="margin: 0;">-<span id="LC2735" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">{</span></span>
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2736
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<pre style="margin: 0;">-<span id="LC2736" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">current_file</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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2737
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<pre style="margin: 0;">-<span id="LC2737" class="line" lang="cpp"><span class="p">}</span></span>
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2738
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<pre style="margin: 0;">-<span id="LC2738" class="line" lang="cpp"></span>
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2739
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2761
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<pre style="margin: 0;"> <span id="LC2761" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// move constructor</span></span>
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2740
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<pre style="margin: 0;">-<span id="LC2740" class="line" lang="cpp"><span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">o</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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2762
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<pre style="margin: 0;">+<span id="LC2762" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if 1</span></span>
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2763
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<pre style="margin: 0;">+<span id="LC2763" class="line" lang="cpp"><span class="n" style="color: #333;">FastqSequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FastqSequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">FastqSequenceReader</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">o</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2764" 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">
2764
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<pre style="margin: 0;">+<span id="LC2764" class="line" lang="cpp"> <span class="n" style="color: #333;">nfiles</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span><span class="p">),</span></span>
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2765
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<pre style="margin: 0;">+<span id="LC2765" class="line" lang="cpp"> <span class="n" style="color: #333;">numreads</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">numreads</span><span class="p">),</span></span>
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2741
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2766
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<pre style="margin: 0;"> <span id="LC2766" class="line" lang="cpp"> <span class="n" style="color: #333;">fp</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">fp</span><span class="p">)),</span></span>
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2742
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<pre style="margin: 0;">-<span id="LC2742" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)),</span></span>
</pre>
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2743
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2767
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<pre style="margin: 0;"> <span id="LC2767" class="line" lang="cpp"> <span class="n" style="color: #333;">l</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">)),</span></span>
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2744
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2768
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<pre style="margin: 0;"> <span id="LC2768" class="line" lang="cpp"> <span class="n" style="color: #333;">nl</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">nl</span><span class="p">)),</span></span>
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2745
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2769
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<pre style="margin: 0;"> <span id="LC2769" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">paired</span><span class="p">),</span></span>
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2746
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<pre style="margin: 0;">-<span id="LC2746" class="line" lang="cpp"> <span class="n" style="color: #333;">nfiles</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span><span class="p">),</span></span>
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2747
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2770
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<pre style="margin: 0;"> <span id="LC2770" class="line" lang="cpp"> <span class="n" style="color: #333;">files</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">)),</span></span>
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2748
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2771
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<pre style="margin: 0;"> <span id="LC2771" class="line" lang="cpp"> <span class="n" style="color: #333;">umi_files</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">umi_files</span><span class="p">)),</span></span>
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2749
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2772
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<pre style="margin: 0;"> <span id="LC2772" class="line" lang="cpp"> <span class="n" style="color: #333;">f_umi</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">f_umi</span><span class="p">)),</span></span>
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2750
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<pre style="margin: 0;">-<span id="LC2750" class="line" lang="cpp"> <span class="n" style="color: #333;">current_file</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">current_file</span><span class="p">),</span></span>
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2751
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<td class="diff-line-num new_line old" data-linenumber="2773" 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="LC2751" class="line" lang="cpp"> <span class="n" style="color: #333;">state</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">state</span><span class="p">)</span> <span class="p">{</span></span>
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2773
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<pre style="margin: 0;">+<span id="LC2773" class="line" lang="cpp"> <span class="n" style="color: #333;">current_file</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">current_file</span><span class="p">)</span> <span class="p">{</span></span>
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2774
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<pre style="margin: 0;">+<span id="LC2774" class="line" lang="cpp"></span>
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2775
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<pre style="margin: 0;">+<span id="LC2775" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">fp</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">);</span></span>
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2776
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<pre style="margin: 0;">+<span id="LC2776" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2777
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<pre style="margin: 0;">+<span id="LC2777" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">nl</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2778" 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">
2778
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<pre style="margin: 0;">+<span id="LC2778" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2752" 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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2779
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<pre style="margin: 0;">+<span id="LC2779" class="line" lang="cpp"><span class="p">}</span></span>
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2780
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<pre style="margin: 0;">+<span id="LC2780" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2781
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<pre style="margin: 0;">+<span id="LC2781" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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2782
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<pre style="margin: 0;">+<span id="LC2782" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">FastqSequenceReader::FastqSequenceReader(FastqSequenceReader&& o) {</span></span>
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2783
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<pre style="margin: 0;">+<span id="LC2783" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> fp = (std::move(o.fp));</span></span>
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2784
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<pre style="margin: 0;">+<span id="LC2784" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> l = (std::move(o.l));</span></span>
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2785
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<pre style="margin: 0;">+<span id="LC2785" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> nl = (std::move(o.nl));</span></span>
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2786
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<pre style="margin: 0;">+<span id="LC2786" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> paired = (o.paired);</span></span>
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2787
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<pre style="margin: 0;">+<span id="LC2787" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> nfiles = (o.nfiles);</span></span>
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2788
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<pre style="margin: 0;">+<span id="LC2788" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> files = (std::move(o.files)),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2789" 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">
2789
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<pre style="margin: 0;">+<span id="LC2789" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> umi_files = (std::move(o.umi_files));</span></span>
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2790
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<pre style="margin: 0;">+<span id="LC2790" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> f_umi = (std::move(o.f_umi));</span></span>
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2791
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<pre style="margin: 0;">+<span id="LC2791" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> current_file= (o.current_file);</span></span>
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2792
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<pre style="margin: 0;">+<span id="LC2792" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> seq = (std::move(o.seq));</span></span>
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2752
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2793
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<pre style="margin: 0;"> <span id="LC2793" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="2753" 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">
2753
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<td class="diff-line-num new_line" data-linenumber="2794" 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">
2794
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<pre style="margin: 0;"> <span id="LC2794" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> o.fp.resize(nfiles);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2754" 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">
2754
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<td class="diff-line-num new_line old" data-linenumber="2795" 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="LC2754" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2755" 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">
2755
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2795
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<pre style="margin: 0;"> <span id="LC2795" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> o.l.resize(nfiles, 0);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2756" 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">
2756
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<td class="diff-line-num new_line" data-linenumber="2796" 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">
2796
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<pre style="margin: 0;"> <span id="LC2796" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> o.nl.resize(nfiles, 0);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2757" 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">
2757
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<td class="diff-line-num new_line" data-linenumber="2797" 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">
2797
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<pre style="margin: 0;"> <span id="LC2797" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> o.state = false;</span></span>
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2798
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<pre style="margin: 0;">+<span id="LC2798" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> o.seq.resize(nfiles, nullptr);</span></span>
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2799
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<pre style="margin: 0;">+<span id="LC2799" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">}</span></span>
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2800
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<pre style="margin: 0;">+<span id="LC2800" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2801" 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">
2801
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<pre style="margin: 0;">+<span id="LC2801" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">BamSequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">seq_enc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"=ACMGRSVTWYHKDBN"</span><span class="p">;</span></span>
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2802
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<pre style="margin: 0;">+<span id="LC2802" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="2803" 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">
2803
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<pre style="margin: 0;">+<span id="LC2803" class="line" lang="cpp"><span class="n" style="color: #333;">BamSequenceReader</span><span class="o" style="font-weight: 600;">::~</span><span class="n" style="color: #333;">BamSequenceReader</span><span class="p">()</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2804" 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">
2804
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<pre style="margin: 0;">+<span id="LC2804" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2805" 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">
2805
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<pre style="margin: 0;">+<span id="LC2805" class="line" lang="cpp"> <span class="n" style="color: #333;">bgzf_close</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2806" 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">
2806
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<pre style="margin: 0;">+<span id="LC2806" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2758" 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="2807" 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">
2807
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<pre style="margin: 0;">+<span id="LC2807" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">head</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2808" 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">
2808
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<pre style="margin: 0;">+<span id="LC2808" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">head</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2809" 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">
2809
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<pre style="margin: 0;">+<span id="LC2809" class="line" lang="cpp"> <span class="p">}</span></span>
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2810
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<pre style="margin: 0;">+<span id="LC2810" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span> <span class="p">{</span></span>
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2811
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<pre style="margin: 0;">+<span id="LC2811" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_destroy1</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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2812
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<pre style="margin: 0;">+<span id="LC2812" class="line" lang="cpp"> <span class="p">}</span></span>
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2813
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<pre style="margin: 0;">+<span id="LC2813" class="line" lang="cpp"><span class="p">}</span></span>
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2814
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<pre style="margin: 0;">+<span id="LC2814" class="line" lang="cpp"></span>
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2815
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<pre style="margin: 0;">+<span id="LC2815" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">BamSequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="p">{</span></span>
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2816
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<pre style="margin: 0;">+<span id="LC2816" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">state</span><span class="p">;</span></span>
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2817
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<pre style="margin: 0;">+<span id="LC2817" class="line" lang="cpp"><span class="p">}</span></span>
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2818
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<pre style="margin: 0;">+<span id="LC2818" class="line" lang="cpp"></span>
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2819
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<pre style="margin: 0;">+<span id="LC2819" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BamSequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reset</span><span class="p">()</span> <span class="p">{</span></span>
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2820
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<pre style="margin: 0;">+<span id="LC2820" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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2821
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<pre style="margin: 0;">+<span id="LC2821" class="line" lang="cpp"><span class="p">}</span></span>
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2822
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<pre style="margin: 0;">+<span id="LC2822" class="line" lang="cpp"></span>
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2823
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<pre style="margin: 0;">+<span id="LC2823" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BamSequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reserveNfiles</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="p">{</span></span>
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2824
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<pre style="margin: 0;">+<span id="LC2824" class="line" lang="cpp"><span class="p">}</span></span>
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2825
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<pre style="margin: 0;">+<span id="LC2825" class="line" lang="cpp"></span>
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2826
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<pre style="margin: 0;">+<span id="LC2826" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// returns true if there is more left to read from the files</span></span>
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2827
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<pre style="margin: 0;">+<span id="LC2827" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">BamSequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limit</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span></span>
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2828
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<pre style="margin: 0;">+<span id="LC2828" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">names</span><span class="p">,</span></span>
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2829
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<pre style="margin: 0;">+<span id="LC2829" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">quals</span><span class="p">,</span></span>
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2830
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<pre style="margin: 0;">+<span id="LC2830" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">flags</span><span class="p">,</span></span>
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2831
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<pre style="margin: 0;">+<span id="LC2831" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">umis</span><span class="p">,</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;">read_id</span><span class="p">,</span></span>
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2832
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<pre style="margin: 0;">+<span id="LC2832" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">full</span><span class="p">)</span> <span class="p">{</span></span>
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2833
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<pre style="margin: 0;">+<span id="LC2833" class="line" lang="cpp"> </span>
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2834
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<pre style="margin: 0;">+<span id="LC2834" class="line" lang="cpp"> <span class="n" style="color: #333;">readbatch_id</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// increase the batch id</span></span>
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2835
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<pre style="margin: 0;">+<span id="LC2835" class="line" lang="cpp"> <span class="n" style="color: #333;">read_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// copy now because we are inside a lock</span></span>
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2836
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<pre style="margin: 0;">+<span id="LC2836" class="line" lang="cpp"> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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2837
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<pre style="margin: 0;">+<span id="LC2837" class="line" lang="cpp"> <span class="n" style="color: #333;">flags</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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2838
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<pre style="margin: 0;">+<span id="LC2838" class="line" lang="cpp"> </span>
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2839
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<pre style="margin: 0;">+<span id="LC2839" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bufpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2840
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<pre style="margin: 0;">+<span id="LC2840" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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2841
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<pre style="margin: 0;">+<span id="LC2841" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">state</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// should we open a file</span></span>
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2842
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<pre style="margin: 0;">+<span id="LC2842" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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2843
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<pre style="margin: 0;">+<span id="LC2843" class="line" lang="cpp"> <span class="p">}</span></span>
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2844
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<pre style="margin: 0;">+<span id="LC2844" class="line" lang="cpp"></span>
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2845
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<pre style="margin: 0;">+<span id="LC2845" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the file is open and we have read into seq1 and seq2</span></span>
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2846
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<pre style="margin: 0;">+<span id="LC2846" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2847
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<pre style="margin: 0;">+<span id="LC2847" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FSECONDARY</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// record is primary alignment</span></span>
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2848
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<pre style="margin: 0;">+<span id="LC2848" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bufadd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l_seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l_bc</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l_umi</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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2849
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<pre style="margin: 0;">+<span id="LC2849" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fits into the buffer</span></span>
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2850
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<pre style="margin: 0;">+<span id="LC2850" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bufpos</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bufadd</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">limit</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2851" 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">
2851
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<pre style="margin: 0;">+<span id="LC2851" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pi</span><span class="p">;</span></span>
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2852
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<pre style="margin: 0;">+<span id="LC2852" class="line" lang="cpp"></span>
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2853
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<pre style="margin: 0;">+<span id="LC2853" class="line" lang="cpp"> <span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bufpos</span><span class="p">;</span></span>
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2854
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<pre style="margin: 0;">+<span id="LC2854" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">pi</span><span class="p">,</span> <span class="n" style="color: #333;">bc</span><span class="p">,</span> <span class="n" style="color: #333;">l_bc</span><span class="p">);</span></span>
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2855
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<pre style="margin: 0;">+<span id="LC2855" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l_bc</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">l_umi</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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2856
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<pre style="margin: 0;">+<span id="LC2856" class="line" lang="cpp"> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">pi</span><span class="p">,</span> <span class="n" style="color: #333;">l_bc</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l_umi</span><span class="p">);</span></span>
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2857
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<pre style="margin: 0;">+<span id="LC2857" class="line" lang="cpp"> <span class="n" style="color: #333;">bufpos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">l_bc</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">l_umi</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2858
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<pre style="margin: 0;">+<span id="LC2858" class="line" lang="cpp"></span>
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2859
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<pre style="margin: 0;">+<span id="LC2859" class="line" lang="cpp"> <span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bufpos</span><span class="p">;</span></span>
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2860
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<pre style="margin: 0;">+<span id="LC2860" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">l_seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2861" 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">
2861
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<pre style="margin: 0;">+<span id="LC2861" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l_seq</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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2862
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<pre style="margin: 0;">+<span id="LC2862" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2863" 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">
2863
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<pre style="margin: 0;">+<span id="LC2863" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">eseq</span><span class="p">)</span> <span class="p">{</span></span>
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2864
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<pre style="margin: 0;">+<span id="LC2864" class="line" lang="cpp"> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="n" style="color: #333;">bufpos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_enc</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eseq</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2865" 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">
2865
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<pre style="margin: 0;">+<span id="LC2865" class="line" lang="cpp"> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="n" style="color: #333;">bufpos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_enc</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eseq</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x0F</span><span class="p">];</span></span>
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2866
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<pre style="margin: 0;">+<span id="LC2866" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2867" 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">
2867
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<pre style="margin: 0;">+<span id="LC2867" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l_seq</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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2868
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<pre style="margin: 0;">+<span id="LC2868" class="line" lang="cpp"> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="n" style="color: #333;">bufpos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq_enc</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eseq</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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2869
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<pre style="margin: 0;">+<span id="LC2869" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2870" 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">
2870
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<pre style="margin: 0;">+<span id="LC2870" class="line" lang="cpp"> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="n" style="color: #333;">bufpos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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2871
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<pre style="margin: 0;">+<span id="LC2871" class="line" lang="cpp"> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">pi</span><span class="p">,</span> <span class="n" style="color: #333;">l_seq</span><span class="p">);</span></span>
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2872
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<pre style="margin: 0;">+<span id="LC2872" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="2873" 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">
2873
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<pre style="margin: 0;">+<span id="LC2873" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2874" 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">
2874
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<pre style="margin: 0;">+<span id="LC2874" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// read it next time</span></span>
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2875
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<pre style="margin: 0;">+<span id="LC2875" class="line" lang="cpp"> <span class="p">}</span></span>
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2876
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<pre style="margin: 0;">+<span id="LC2876" class="line" lang="cpp"> <span class="p">}</span></span>
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2877
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<pre style="margin: 0;">+<span id="LC2877" class="line" lang="cpp"> </span>
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2878
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<pre style="margin: 0;">+<span id="LC2878" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// read for the next one</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2879" 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">
2879
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<pre style="margin: 0;">+<span id="LC2879" class="line" lang="cpp"> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_read1</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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2880
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<pre style="margin: 0;">+<span id="LC2880" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2881" 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">
2881
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<pre style="margin: 0;">+<span id="LC2881" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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2882
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<pre style="margin: 0;">+<span id="LC2882" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2883" 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">
2883
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<pre style="margin: 0;">+<span id="LC2883" class="line" lang="cpp"> <span class="n" style="color: #333;">eseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_seq</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2884" 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">
2884
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<pre style="margin: 0;">+<span id="LC2884" class="line" lang="cpp"> <span class="n" style="color: #333;">l_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">;</span></span>
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2885
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<pre style="margin: 0;">+<span id="LC2885" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="2886" 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">
2886
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<pre style="margin: 0;">+<span id="LC2886" class="line" lang="cpp"> <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_aux2Z</span><span class="p">(</span><span class="n" style="color: #333;">bam_aux_get</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CR"</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2887" 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">
2887
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<pre style="margin: 0;">+<span id="LC2887" class="line" lang="cpp"> <span class="n" style="color: #333;">l_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2888" 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">
2888
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<pre style="margin: 0;">+<span id="LC2888" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pbc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pbc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pbc</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2889" 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">
2889
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<pre style="margin: 0;">+<span id="LC2889" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l_bc</span><span class="p">;</span></span>
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2890
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<pre style="margin: 0;">+<span id="LC2890" class="line" lang="cpp"> <span class="p">}</span></span>
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2891
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<pre style="margin: 0;">+<span id="LC2891" class="line" lang="cpp"></span>
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2892
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<pre style="margin: 0;">+<span id="LC2892" class="line" lang="cpp"> <span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_aux2Z</span><span class="p">(</span><span class="n" style="color: #333;">bam_aux_get</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"UR"</span><span class="p">));</span></span>
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2893
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<pre style="margin: 0;">+<span id="LC2893" class="line" lang="cpp"> <span class="n" style="color: #333;">l_umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2894
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<pre style="margin: 0;">+<span id="LC2894" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pumi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">umi</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pumi</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pumi</span><span class="p">)</span> <span class="p">{</span></span>
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2895
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<pre style="margin: 0;">+<span id="LC2895" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l_umi</span><span class="p">;</span></span>
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2896
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<pre style="margin: 0;">+<span id="LC2896" class="line" lang="cpp"> <span class="p">}</span></span>
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2897
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<pre style="margin: 0;">+<span id="LC2897" class="line" lang="cpp"></span>
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2898
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<pre style="margin: 0;">+<span id="LC2898" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2899
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<pre style="margin: 0;">+<span id="LC2899" class="line" lang="cpp"> <span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// haven't opened file yet</span></span>
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2900
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<pre style="margin: 0;">+<span id="LC2900" class="line" lang="cpp"> <span class="p">}</span></span>
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2901
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<pre style="margin: 0;">+<span id="LC2901" class="line" lang="cpp"> <span class="p">}</span></span>
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2758
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2902
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<pre style="margin: 0;"> <span id="LC2902" class="line" lang="cpp"><span class="p">}</span></span>
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2903
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<pre style="margin: 0;">+<span id="LC2903" class="line" lang="cpp"></span></pre>
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<li id="c9d576083b226885d32fcec0ac23456a74eb4060">
<a href="https://salsa.debian.org/med-team/kallisto/compare/be9e6cf5d8ad9f0c90b203b70c88d5c92793871f...79ce01c1e7c21ef09950fa0c79e02cac2c6abcca#c9d576083b226885d32fcec0ac23456a74eb4060"><strong>src/ProcessReads.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,6 +23,7 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "GeneModel.h"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "BUSData.h"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "BUSTools.h"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/sam.h></span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef KSEQ_INIT_READY</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">@@ -41,9 +42,35 @@ class SequenceReader {</td>
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41
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">opt</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">single_end</span><span class="p">),</span> <span class="n" style="color: #333;">files</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">f_umi</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span><span class="p">{}),</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">current_file</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">state</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">readbatch_id</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{};</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">state</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{};</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">SequenceReader</span><span class="p">()</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// SequenceReader(SequenceReader&& o);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reserveNfiles</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limit</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">seqs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">names</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">quals</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">flags</span><span class="p">,</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">umis</span><span class="p">,</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;">readbatch_id</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">full</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">state</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// is the file open</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">readbatch_id</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="p">;</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastqSequenceReader</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">SequenceReader</span> <span class="p">{</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"><span class="nl">public:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">FastqSequenceReader</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">opt</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">SequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">),</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">current_file</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">paired</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">single_end</span><span class="p">),</span> <span class="n" style="color: #333;">files</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">),</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">f_umi</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span><span class="p">{})</span> <span class="p">{</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"></span>
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47
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bus_mode</span><span class="p">)</span> <span class="p">{</span></span>
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48
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span><span class="p">;</span> </span>
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49
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,46 +78,106 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">reserveNfiles</span><span class="p">(</span><span class="n" style="color: #333;">nfiles</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">SequenceReader</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">FastqSequenceReader</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">SequenceReader</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span> </span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">f_umi</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span><span class="p">{}),</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">current_file</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">state</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span> <span class="n" style="color: #333;">readbatch_id</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">o</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">empty</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">current_file</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{};</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">FastqSequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">FastqSequenceReader</span> <span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;">o</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">FastqSequenceReader</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">empty</span><span class="p">();</span> </span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reserveNfiles</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">SequenceReader</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limit</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">seqs</span><span class="p">,</span></span>
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">names</span><span class="p">,</span></span>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">quals</span><span class="p">,</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">flags</span><span class="p">,</span></span>
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">umis</span><span class="p">,</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;">readbatch_id</span><span class="p">,</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">full</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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70
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"></span>
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71
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"><span class="nl">public:</span></span>
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72
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">numreads</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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73
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">gzFile</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fp</span><span class="p">;</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//gzFile fp1 = 0, fp2 = 0;</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">kseq_t</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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76
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">l</span><span class="p">;</span></span>
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77
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">nl</span><span class="p">;</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//kseq_t *seq1 = 0, *seq2 = 0;</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//int l1,l2,nl1,nl2;</span></span>
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80
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">paired</span><span class="p">;</span></span>
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81
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">files</span><span class="p">;</span></span>
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82
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">umi_files</span><span class="p">;</span></span>
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83
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ifstream</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">f_umi</span><span class="p">;</span></span>
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84
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">current_file</span><span class="p">;</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">state</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// is the file open</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">readbatch_id</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="p">;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">kseq_t</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"><span class="p">};</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BamSequenceReader</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">SequenceReader</span> <span class="p">{</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"><span class="nl">public:</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">BamSequenceReader</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">opt</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">)</span> <span class="p">{</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bgzf_open</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">head</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_init1</span><span class="p">();</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> </span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_read1</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">eseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_seq</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">l_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">l_qseq</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_aux2Z</span><span class="p">(</span><span class="n" style="color: #333;">bam_aux_get</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"CR"</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">l_bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pbc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bc</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pbc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pbc</span><span class="p">)</span> <span class="p">{</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l_bc</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="p">}</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_aux2Z</span><span class="p">(</span><span class="n" style="color: #333;">bam_aux_get</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">"UR"</span><span class="p">));</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">l_umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pumi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">umi</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pumi</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pumi</span><span class="p">)</span> <span class="p">{</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l_umi</span><span class="p">;</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="p">}</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="p">}</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">BamSequenceReader</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">SequenceReader</span><span class="p">()</span> <span class="p">{};</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">BamSequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">BamSequenceReader</span> <span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;">o</span><span class="p">);</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">BamSequenceReader</span><span class="p">();</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> </span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">empty</span><span class="p">();</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reserveNfiles</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fetchSequences</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">limit</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">seqs</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">names</span><span class="p">,</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">quals</span><span class="p">,</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">flags</span><span class="p">,</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">umis</span><span class="p">,</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;">readbatch_id</span><span class="p">,</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">full</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"><span class="nl">public:</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">BGZF</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span><span class="p">;</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_hdr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">head</span><span class="p">;</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">bam1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rec</span><span class="p">;</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">eseq</span><span class="p">;</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">l_seq</span><span class="p">;</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bc</span><span class="p">;</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l_bc</span><span class="p">;</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">umi</span><span class="p">;</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l_umi</span><span class="p">;</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">err</span><span class="p">;</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// Is there a better limit?</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> </span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"><span class="nl">private:</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq_enc</span><span class="p">;</span></span>
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87
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"><span class="p">};</span></span>
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88
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"></span>
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89
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MasterProcessor</span> <span class="p">{</span></span>
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90
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"><span class="nl">public:</span></span>
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91
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">MasterProcessor</span> <span class="p">(</span><span class="n" style="color: #333;">KmerIndex</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">MinCollector</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Transcriptome</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">model</span><span class="p">)</span></span>
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<td class="diff-line-num new_line old" data-linenumber="173" 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="LC92" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tc</span><span class="p">(</span><span class="n" style="color: #333;">tc</span><span class="p">),</span> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">model</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">),</span> <span class="n" style="color: #333;">bamfp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">bamfps</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">bamh</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">opt</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">),</span> <span class="n" style="color: #333;"><span class="idiff left">SR</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">numreads</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tc</span><span class="p">(</span><span class="n" style="color: #333;">tc</span><span class="p">),</span> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">model</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">),</span> <span class="n" style="color: #333;">bamfp</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">bamfps</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">bamh</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">),</span> <span class="n" style="color: #333;">opt</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">),</span> <span class="n" style="color: #333;">numreads</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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93
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<td class="diff-line-num new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="p">,</span><span class="n" style="color: #333;">nummapped</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">num_umi</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">bufsize</span><span class="p">(</span><span class="mi" style="color: #099;">1ULL</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">23</span><span class="p">),</span> <span class="n" style="color: #333;">tlencount</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">biasCount</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">maxBiasCount</span><span class="p">((</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bias</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1000000</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">last_pseudobatch_id</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">SR</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BamSequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">SR</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastqSequenceReader</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="p">}</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"></span>
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94
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_mode</span><span class="p">)</span> <span class="p">{</span></span>
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95
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bus_bc_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">33</span><span class="p">);</span></span>
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96
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bus_umi_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">33</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="136" 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="223" 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">@@ -136,13 +223,14 @@ public:</td>
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136
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">bam_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">bamh</span><span class="p">);</span></span>
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137
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="n" style="color: #333;">bamh</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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138
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="p">}</span> </span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">SR</span><span class="p">;</span></span>
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139
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span> <span class="n" style="color: #333;">reader_lock</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span> <span class="n" style="color: #333;">writer_lock</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span> <span class="n" style="color: #333;">SR</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">SR</span><span class="p">;</span></span>
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"> <span class="n" style="color: #333;">MinCollector</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">KmerIndex</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Transcriptome</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">model</span><span class="p">;</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">@@ -205,7 +293,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">new_ec_umi</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">KmerIndex</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">MasterProcessor</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span> <span class="n" style="color: #333;">batchSR</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">Fastq</span>SequenceReader</span> <span class="n" style="color: #333;">batchSR</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">numreads</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">local_id</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -215,6 +303,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">seqs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">names</span><span class="p">;</span></span>
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">quals</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">flags</span><span class="p">;</span></span>
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">umis</span><span class="p">;</span></span>
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">newEcs</span><span class="p">;</span></span>
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">flens</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="237" 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">@@ -237,6 +326,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">bufsize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">paired</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">bam</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">num</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">MinCollector</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">KmerIndex</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">MasterProcessor</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mp</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="251" 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">@@ -251,6 +342,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">seqs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">names</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">quals</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">flags</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">newEcs</span><span class="p">;</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</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;">flens</span><span class="p">;</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">@@ -279,7 +371,7 @@ public:</td>
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">KmerIndex</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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280
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EMAlgorithm</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">em</span><span class="p">;</span></span>
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281
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">MasterProcessor</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mp</span><span class="p">;</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">SequenceReader</span> <span class="n" style="color: #333;">batchSR</span><span class="p">;</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">Fastq</span>SequenceReader</span> <span class="n" style="color: #333;">batchSR</span><span class="p">;</span></span>
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283
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">numreads</span><span class="p">;</span></span>
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">PseudoAlignmentBatch</span> <span class="n" style="color: #333;">pseudobatch</span><span class="p">;</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">@@ -291,6 +383,7 @@ public:</td>
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">seqs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">names</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</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;">quals</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">flags</span><span class="p">;</span></span>
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">umis</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="k" style="font-weight: 600;">operator</span><span class="p">()();</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef KALLISTO_COMMON_H</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KALLISTO_COMMON_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KALLISTO_VERSION "0.46.<span class="idiff left right">0</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KALLISTO_VERSION "0.46.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _WIN64</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">uint</span><span class="p">;</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">@@ -67,6 +67,8 @@ struct ProgramOptions {</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">bus_mode</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">BUSOptions</span> <span class="n" style="color: #333;">busOptions</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">pseudo_quant</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">bam</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">num</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">batch_file_name</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">batch_files</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">batch_ids</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="109" 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">@@ -107,6 +109,8 @@ ProgramOptions() :</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">batch_mode</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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108
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">bus_mode</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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109
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">pseudo_quant</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">bam</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">num</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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110
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<td class="diff-line-num new_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">plaintext</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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111
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<td class="diff-line-num new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">write_index</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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112
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"> <span class="n" style="color: #333;">single_end</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<li id="b958235ee8db37bcaceda04b6d55553b450c2db4">
<a href="https://salsa.debian.org/med-team/kallisto/compare/be9e6cf5d8ad9f0c90b203b70c88d5c92793871f...79ce01c1e7c21ef09950fa0c79e02cac2c6abcca#b958235ee8db37bcaceda04b6d55553b450c2db4"><strong>src/main.cpp</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">@@ -533,20 +533,24 @@ void ListSingleCellTechnologies() {</td>
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533
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<td class="diff-line-num new_line" data-linenumber="533" 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">
533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"CELSeq CEL-Seq"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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534
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<td class="diff-line-num new_line" data-linenumber="534" 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">
534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"CELSeq2 CEL-Seq version 2"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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535
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<td class="diff-line-num new_line" data-linenumber="535" 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">
535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"DropSeq DropSeq"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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536
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<td class="diff-line-num new_line old" data-linenumber="536" 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="LC536" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"inDrops inDrops"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"inDropsv1 inDrops version 1 chemistry"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"inDropsv2 inDrops version 2 chemistry"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"inDropsv3 inDrops version 3 chemistry"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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537
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SCRBSeq SCRB-Seq"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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538
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SureCell SureCell for ddSEQ"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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539
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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540
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp"> <span class="p">}</span></span>
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541
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"></span>
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542
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ParseOptionsBus</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">opt</span><span class="p">)</span> <span class="p">{</span></span>
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543
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opt_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:o:x:t:l"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opt_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"i:o:x:t:l<span class="idiff left right">bn</span>"</span><span class="p">;</span></span>
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544
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">long_options</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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545
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"index"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">},</span></span>
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546
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"output-dir"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span></span>
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547
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549
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"technology"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">},</span></span>
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548
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550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"list"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">},</span></span>
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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">},</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bam"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'b'</span><span class="p">},</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"num"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">},</span></span>
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="cpp"> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="cpp"> <span class="p">};</span></span>
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="584" 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">@@ -584,6 +588,14 @@ void ParseOptionsBus(int argc, char **argv, ProgramOptions& opt) {</td>
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584
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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585
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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586
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="cpp"> <span class="p">}</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'b'</span><span class="p">:</span> <span class="p">{</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">:</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="p">}</span></span>
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="cpp"> <span class="nl">default:</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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600
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="cpp"> <span class="p">}</span></span>
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601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp"> <span class="p">}</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">@@ -812,84 +824,183 @@ bool CheckOptionsBus(ProgramOptions& opt) {</td>
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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813
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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814
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826
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">busopt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">busOptions</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"10XV2"</span><span class="p">)</span> <span class="p">{</span></span>
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817
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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818
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// second file, entire string</span></span>
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<td class="diff-line-num old old_line" data-linenumber="819" 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">
819
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<pre style="margin: 0;">-<span id="LC819" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">,</span><span class="mi" style="color: #099;">26</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// first file [16:26]</span></span>
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<pre style="margin: 0;">-<span id="LC820" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">));</span></span>
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821
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<pre style="margin: 0;">-<span id="LC821" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"10XV3"</span><span class="p">)</span> <span class="p">{</span></span>
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822
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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823
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">,</span><span class="mi" style="color: #099;">28</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">));</span></span>
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826
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"10XV1"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="827" 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">
827
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC827" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="828" 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">
828
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC828" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="829" 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">
829
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC829" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="830" 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">
830
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC830" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="831" 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">
831
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC831" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"SURECELL"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="832" 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">
832
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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833
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="834" 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">
834
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC834" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">51</span><span class="p">,</span><span class="mi" style="color: #099;">59</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="835" 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">
835
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC835" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="836" 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">
836
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC836" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">21</span><span class="p">,</span><span class="mi" style="color: #099;">27</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="837" 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">
837
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC837" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="838" 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">
838
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC838" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DROPSEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="839" 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">
839
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC839" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="840" 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">
840
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC840" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="841" 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">
841
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC841" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="842" 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">
842
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC842" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="843" 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">
843
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<td class="diff-line-num new_line old" data-linenumber="827" 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="LC843" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INDROPS"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="844" 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">
844
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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845
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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846
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<pre style="margin: 0;">-<span id="LC846" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">);</span></span>
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847
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">11</span><span class="p">));</span></span>
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848
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">,</span><span class="mi" style="color: #099;">38</span><span class="p">));</span> </span>
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849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"CELSEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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850
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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851
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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852
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<pre style="margin: 0;">-<span id="LC852" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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853
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<pre style="margin: 0;">-<span id="LC853" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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854
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"CELSEQ2"</span><span class="p">)</span> <span class="p">{</span></span>
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855
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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856
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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857
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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858
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">));</span></span>
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859
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"SCRBSEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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860
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<pre style="margin: 0;">-<span id="LC860" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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861
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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862
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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863
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">));</span></span>
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864
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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865
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</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;">files</span><span class="p">;</span></span>
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866
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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867
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bcValues</span><span class="p">;</span></span>
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868
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">errorList</span><span class="p">;</span></span>
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869
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<pre style="margin: 0;">-<span id="LC869" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">invalid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParseTechnology</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">files</span><span class="p">,</span> <span class="n" style="color: #333;">errorList</span><span class="p">,</span> <span class="n" style="color: #333;">bcValues</span><span class="p">);</span></span>
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870
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">invalid</span><span class="p">)</span> <span class="p">{</span></span>
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871
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> </span>
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872
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bcValues</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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873
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">bcValues</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="cpp"> </span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Note: only 10xV2 has been tested</span></span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"10XV2"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="831" 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">
831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// second file, entire string</span></span>
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<td class="diff-line-num new new_line" data-linenumber="832" 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">
832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">,</span><span class="mi" style="color: #099;">26</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// first file [16:26]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="833" 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">
833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">));</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"10XV3"</span><span class="p">)</span> <span class="p">{</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">,</span><span class="mi" style="color: #099;">28</span><span class="p">);</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">));</span></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// } else if (opt.technology == "10XV1") {</span></span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="cpp"></span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"SURECELL"</span><span class="p">)</span> <span class="p">{</span></span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">18</span><span class="p">,</span><span class="mi" style="color: #099;">26</span><span class="p">);</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">18</span><span class="p">));</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DROPSEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">);</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">));</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INDROPSV1"</span><span class="p">)</span> <span class="p">{</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">);</span></span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">11</span><span class="p">));</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">,</span><span class="mi" style="color: #099;">38</span><span class="p">));</span> </span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INDROPSV2"</span><span class="p">)</span> <span class="p">{</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">);</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">11</span><span class="p">));</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">,</span><span class="mi" style="color: #099;">38</span><span class="p">));</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="860" 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">
860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INDROPSV3"</span><span class="p">)</span> <span class="p">{</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="862" 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">
862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="863" 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">
863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">,</span><span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="864" 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">
864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="865" 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">
865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="866" 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">
866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"CELSEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="867" 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">
867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="868" 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">
868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"CELSEQ2"</span><span class="p">)</span> <span class="p">{</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">));</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"SCRBSEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">));</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INDROPSV3"</span><span class="p">)</span> <span class="p">{</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">));</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</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;">files</span><span class="p">;</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bcValues</span><span class="p">;</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">errorList</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">invalid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParseTechnology</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">files</span><span class="p">,</span> <span class="n" style="color: #333;">errorList</span><span class="p">,</span> <span class="n" style="color: #333;">bcValues</span><span class="p">);</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">invalid</span><span class="p">)</span> <span class="p">{</span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> </span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bcValues</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">bcValues</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="cpp"> <span class="p">}</span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">errorList</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="cpp"> <span class="p">}</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Unable to create technology: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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874
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901
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="cpp"> <span class="p">}</span></span>
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875
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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876
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="cpp"> <span class="p">}</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"10XV2"</span><span class="p">)</span> <span class="p">{</span></span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// second file, entire string</span></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">,</span><span class="mi" style="color: #099;">26</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// first file [16:26]</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">));</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="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"10XV3"</span><span class="p">)</span> <span class="p">{</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">,</span><span class="mi" style="color: #099;">28</span><span class="p">);</span></span>
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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="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="914" 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">
914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"10XV1"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="915" 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">
915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="916" 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">
916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</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="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="919" 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">
919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"SURECELL"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="920" 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">
920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="921" 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">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="922" 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">
922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">51</span><span class="p">,</span><span class="mi" style="color: #099;">59</span><span class="p">);</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="924" 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">
924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">21</span><span class="p">,</span><span class="mi" style="color: #099;">27</span><span class="p">));</span></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="926" 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">
926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DROPSEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="927" 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">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></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="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="929" 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">
929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="930" 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">
930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="931" 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">
931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INDROPSV1"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="932" 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">
932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="933" 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">
933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="934" 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">
934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="935" 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">
935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">11</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="936" 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">
936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">,</span><span class="mi" style="color: #099;">38</span><span class="p">));</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="937" 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">
937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INDROPSV2"</span><span class="p">)</span> <span class="p">{</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="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</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="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">42</span><span class="p">,</span><span class="mi" style="color: #099;">48</span><span class="p">);</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">11</span><span class="p">));</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">30</span><span class="p">,</span><span class="mi" style="color: #099;">38</span><span class="p">));</span> </span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INDROPSV3"</span><span class="p">)</span> <span class="p">{</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">,</span><span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"CELSEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"CELSEQ2"</span><span class="p">)</span> <span class="p">{</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">);</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">));</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"SCRBSEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="961" 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">
961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="962" 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">
962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">,</span><span class="mi" style="color: #099;">16</span><span class="p">);</span></span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="964" 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">
964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INDROPSV3"</span><span class="p">)</span> <span class="p">{</span></span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="967" 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">
967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">,</span><span class="mi" style="color: #099;">14</span><span class="p">);</span></span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">8</span><span class="p">));</span></span>
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877
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<td class="diff-line-num 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">
970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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878
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<td class="diff-line-num new_line old" data-linenumber="971" 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="LC878" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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879
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<td class="diff-line-num new_line old" data-linenumber="971" 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="LC879" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">errorList</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</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;">files</span><span class="p">;</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bcValues</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="974" 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">
974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">errorList</span><span class="p">;</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">invalid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParseTechnology</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span><span class="p">,</span> <span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">files</span><span class="p">,</span> <span class="n" style="color: #333;">errorList</span><span class="p">,</span> <span class="n" style="color: #333;">bcValues</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="976" 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">
976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">invalid</span><span class="p">)</span> <span class="p">{</span></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</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="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bcValues</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="979" 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">
979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">bcValues</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="981" 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">
981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></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="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</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="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</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="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="985" 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">
985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">errorList</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="987" 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">
987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Unable to create technology: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="988" 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">
988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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880
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989
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<pre style="margin: 0;"> <span id="LC989" class="line" lang="cpp"> <span class="p">}</span></span>
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881
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Unable to create technology: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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882
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<pre style="margin: 0;">-<span id="LC882" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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883
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990
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<pre style="margin: 0;"> <span id="LC990" class="line" lang="cpp"> <span class="p">}</span></span>
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884
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991
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="cpp"> <span class="p">}</span></span>
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992
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="cpp"> <span class="p">}</span></span>
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886
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993
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<pre style="margin: 0;"> <span id="LC993" class="line" lang="cpp"></span>
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887
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bam</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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888
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995
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<pre style="margin: 0;"> <span id="LC995" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: Number of files ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") does not match number of input files required by "</span></span>
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889
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996
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<pre style="margin: 0;"> <span id="LC996" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"technology "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">technology</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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">nfiles</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;">endl</span><span class="p">;</span></span>
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890
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997
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<pre style="margin: 0;"> <span id="LC997" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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891
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998
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<pre style="margin: 0;"> <span id="LC998" class="line" lang="cpp"> <span class="p">}</span></span>
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892
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999
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<pre style="margin: 0;"> <span id="LC999" class="line" lang="cpp"></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">num</span><span class="p">)</span> <span class="p">{</span></span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: --bam option was used, so --num option will be ignored"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="cpp"> <span class="p">}</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="cpp"></span>
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893
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1004
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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894
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1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="cpp"><span class="p">}</span></span>
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895
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1006
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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1535" 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="1646" 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">@@ -1535,7 +1646,9 @@ void usageBus() {</td>
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1535
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<td class="diff-line-num new_line" data-linenumber="1646" 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">
1646
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-x, --technology=STRING Single-cell technology used "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num old_line" data-linenumber="1536" 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">
1536
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<td class="diff-line-num new_line" data-linenumber="1647" 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">
1647
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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Optional arguments:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num old_line" data-linenumber="1537" 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">
1537
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<td class="diff-line-num new_line" data-linenumber="1648" 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">
1648
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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-l, --list List all single-cell technologies supported"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1538" 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">
1538
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<td class="diff-line-num new_line old" data-linenumber="1649" 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="LC1538" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-t, --threads=INT Number of threads to use (default: 1)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1649" 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">
1649
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<pre style="margin: 0;">+<span id="LC1649" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-t, --threads=INT Number of threads to use (default: 1)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1650" 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">
1650
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<pre style="margin: 0;">+<span id="LC1650" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-b, --bam Input file is a BAM file"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1651" 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">
1651
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<pre style="margin: 0;">+<span id="LC1651" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-n, --num Output number of read in flag column (incompatible with --bam)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1539
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1652
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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="cpp"><span class="p">}</span></span>
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1540
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1653
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<pre style="margin: 0;"> <span id="LC1653" class="line" lang="cpp"></span>
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1541
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1654
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<pre style="margin: 0;"> <span id="LC1654" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">usageIndex</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1808" 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="1921" 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">@@ -1808,6 +1921,7 @@ int main(int argc, char *argv[]) {</td>
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1808
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<td class="diff-line-num new_line" data-linenumber="1921" 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">
1921
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<pre style="margin: 0;"> <span id="LC1921" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">num_trans</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1809" 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">
1809
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<td class="diff-line-num new_line" data-linenumber="1922" 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">
1922
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<pre style="margin: 0;"> <span id="LC1922" class="line" lang="cpp"> <span class="n" style="color: #333;">num_unique</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> </span>
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1810
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1923
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<pre style="margin: 0;"> <span id="LC1923" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1924" 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">
1924
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<pre style="margin: 0;">+<span id="LC1924" class="line" lang="cpp"> <span class="n" style="color: #333;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1811
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<td class="diff-line-num new_line" data-linenumber="1925" 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">
1925
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<pre style="margin: 0;"> <span id="LC1925" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1812
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<td class="diff-line-num new_line" data-linenumber="1926" 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">
1926
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<pre style="margin: 0;"> <span id="LC1926" class="line" lang="cpp"> <span class="n" style="color: #333;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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1813
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1927
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<pre style="margin: 0;"> <span id="LC1927" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1953" 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="2067" 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">@@ -1953,6 +2067,10 @@ int main(int argc, char *argv[]) {</td>
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1953
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<td class="diff-line-num new_line" data-linenumber="2067" 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">
2067
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<pre style="margin: 0;"> <span id="LC2067" class="line" lang="cpp"> <span class="n" style="color: #333;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="1954" 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">
1954
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<td class="diff-line-num new_line" data-linenumber="2068" 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">
2068
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<pre style="margin: 0;"> <span id="LC2068" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1955" 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">
1955
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<td class="diff-line-num new_line" data-linenumber="2069" 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">
2069
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<pre style="margin: 0;"> <span id="LC2069" class="line" lang="cpp"></span>
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<td class="diff-line-num new old_line" data-linenumber="1956" 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="2070" 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">
2070
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<pre style="margin: 0;">+<span id="LC2070" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1956" 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="2071" 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">
2071
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<pre style="margin: 0;">+<span id="LC2071" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[~warn] Warning, zero reads pseudoaligned check your input files and index"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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2072
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<pre style="margin: 0;">+<span id="LC2072" class="line" lang="cpp"> <span class="p">}</span></span>
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2073
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<pre style="margin: 0;">+<span id="LC2073" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1956" 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">
1956
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<td class="diff-line-num new_line" data-linenumber="2074" 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">
2074
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<pre style="margin: 0;"> <span id="LC2074" class="line" lang="cpp"> <span class="n" style="color: #333;">plaintext_aux</span><span class="p">(</span></span>
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1957
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<td class="diff-line-num new_line" data-linenumber="2075" 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">
2075
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<pre style="margin: 0;"> <span id="LC2075" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/run_info.json"</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1958" 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">
1958
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<td class="diff-line-num new_line" data-linenumber="2076" 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">
2076
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<pre style="margin: 0;"> <span id="LC2076" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">num_trans</span><span class="p">)),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1968" 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="2086" 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">@@ -1968,7 +2086,17 @@ int main(int argc, char *argv[]) {</td>
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1968
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<td class="diff-line-num new_line" data-linenumber="2086" 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">
2086
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<pre style="margin: 0;"> <span id="LC2086" class="line" lang="cpp"> <span class="n" style="color: #333;">plaintext_writer</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/abundance.tsv"</span><span class="p">,</span> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">target_names_</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1969" 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">
1969
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<td class="diff-line-num new_line" data-linenumber="2087" 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">
2087
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<pre style="margin: 0;"> <span id="LC2087" class="line" lang="cpp"> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">alpha_</span><span class="p">,</span> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">eff_lens_</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">target_lens_</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1970" 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">
1970
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<td class="diff-line-num new_line" data-linenumber="2088" 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">
2088
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<pre style="margin: 0;"> <span id="LC2088" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="1971" 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">
1971
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<td class="diff-line-num new_line old" data-linenumber="2089" 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="LC1971" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1972" 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="2089" 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">
2089
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<pre style="margin: 0;">+<span id="LC2089" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</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;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2090" 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">
2090
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<pre style="margin: 0;">+<span id="LC2090" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this happens if nothing aligns, then we write an empty bootstrap file</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1972" 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="2091" 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">
2091
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<pre style="margin: 0;">+<span id="LC2091" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</span><span class="p">;</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2092" 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">
2092
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<pre style="margin: 0;">+<span id="LC2092" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">plaintext</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2093" 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">
2093
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<pre style="margin: 0;">+<span id="LC2093" class="line" lang="cpp"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">write_bootstrap</span><span class="p">(</span><span class="n" style="color: #333;">em</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// em is empty</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2094" 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">
2094
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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2095" 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">
2095
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<pre style="margin: 0;">+<span id="LC2095" class="line" lang="cpp"> <span class="n" style="color: #333;">plaintext_writer</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/bs_abundance_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".tsv"</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1972" 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="2096" 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">
2096
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<pre style="margin: 0;">+<span id="LC2096" class="line" lang="cpp"> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">target_names_</span><span class="p">,</span> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">alpha_</span><span class="p">,</span> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">eff_lens_</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">target_lens_</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// re-use empty input</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2097" 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">
2097
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<pre style="margin: 0;">+<span id="LC2097" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2098" 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">
2098
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<pre style="margin: 0;">+<span id="LC2098" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2099" 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">
2099
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<pre style="margin: 0;">+<span id="LC2099" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</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;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1972
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<td class="diff-line-num new_line" data-linenumber="2100" 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">
2100
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<pre style="margin: 0;"> <span id="LC2100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">B</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1973" 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">
1973
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2101
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<pre style="margin: 0;"> <span id="LC2101" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mt19937_64</span> <span class="n" style="color: #333;">rand</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1974" 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">
1974
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2102
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<pre style="margin: 0;"> <span id="LC2102" class="line" lang="cpp"> <span class="n" style="color: #333;">rand</span><span class="p">.</span><span class="n" style="color: #333;">seed</span><span class="p">(</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">seed</span> <span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2144" 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">@@ -2016,6 +2144,9 @@ int main(int argc, char *argv[]) {</td>
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2016
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2144
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<pre style="margin: 0;"> <span id="LC2144" class="line" lang="cpp"> </span>
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2017
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<td class="diff-line-num new_line" data-linenumber="2145" 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">
2145
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<pre style="margin: 0;"> <span id="LC2145" class="line" lang="cpp"></span>
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2018
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<td class="diff-line-num new_line" data-linenumber="2146" 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">
2146
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<pre style="margin: 0;"> <span id="LC2146" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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2147
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<pre style="margin: 0;">+<span id="LC2147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2148" 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">
2148
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<pre style="margin: 0;">+<span id="LC2148" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// exit with error</span></span>
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2149
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<pre style="margin: 0;">+<span id="LC2149" class="line" lang="cpp"> <span class="p">}</span></span>
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2019
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<td class="diff-line-num new_line" data-linenumber="2150" 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">
2150
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<pre style="margin: 0;"> <span id="LC2150" class="line" lang="cpp"> <span class="p">}</span></span>
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2020
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<td class="diff-line-num new_line" data-linenumber="2151" 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">
2151
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<pre style="margin: 0;"> <span id="LC2151" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"quant-only"</span><span class="p">)</span> <span class="p">{</span></span>
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2021
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2152
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<pre style="margin: 0;"> <span id="LC2152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2086" 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="2217" 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">@@ -2086,7 +2217,27 @@ int main(int argc, char *argv[]) {</td>
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2086
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2217
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<pre style="margin: 0;"> <span id="LC2217" class="line" lang="cpp"> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">alpha_</span><span class="p">,</span> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">eff_lens_</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">target_lens_</span><span class="p">);</span></span>
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2087
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2218
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<pre style="margin: 0;"> <span id="LC2218" class="line" lang="cpp"> <span class="p">}</span></span>
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2088
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2219
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<pre style="margin: 0;"> <span id="LC2219" class="line" lang="cpp"></span>
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2089
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<pre style="margin: 0;">-<span id="LC2089" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2220
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<pre style="margin: 0;">+<span id="LC2220" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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2221
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<pre style="margin: 0;">+<span id="LC2221" class="line" lang="cpp"></span>
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2222
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<pre style="margin: 0;">+<span id="LC2222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2223
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<pre style="margin: 0;">+<span id="LC2223" class="line" lang="cpp"> <span class="n" style="color: #333;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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2224
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<pre style="margin: 0;">+<span id="LC2224" class="line" lang="cpp"> <span class="p">}</span></span>
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2225
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<pre style="margin: 0;">+<span id="LC2225" class="line" lang="cpp"></span>
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2226
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<pre style="margin: 0;">+<span id="LC2226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2227" 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">
2227
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<pre style="margin: 0;">+<span id="LC2227" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[~warn] Warning, zero reads pseudoaligned check your input files and index"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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2228
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<pre style="margin: 0;">+<span id="LC2228" class="line" lang="cpp"> <span class="p">}</span></span>
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2229
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<pre style="margin: 0;">+<span id="LC2229" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="2230" 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">
2230
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<pre style="margin: 0;">+<span id="LC2230" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</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;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2231" 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">
2231
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<pre style="margin: 0;">+<span id="LC2231" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// this happens if nothing aligns, then we write an empty bootstrap file</span></span>
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2232
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<pre style="margin: 0;">+<span id="LC2232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</span><span class="p">;</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2233" 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">
2233
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<pre style="margin: 0;">+<span id="LC2233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">plaintext</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2234" 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">
2234
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<pre style="margin: 0;">+<span id="LC2234" class="line" lang="cpp"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">write_bootstrap</span><span class="p">(</span><span class="n" style="color: #333;">em</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// em is empty</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2235" 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">
2235
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<pre style="margin: 0;">+<span id="LC2235" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2236" 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">
2236
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<pre style="margin: 0;">+<span id="LC2236" class="line" lang="cpp"> <span class="n" style="color: #333;">plaintext_writer</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/bs_abundance_"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".tsv"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2237" 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">
2237
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<pre style="margin: 0;">+<span id="LC2237" class="line" lang="cpp"> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">target_names_</span><span class="p">,</span> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">alpha_</span><span class="p">,</span> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">eff_lens_</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">target_lens_</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// re-use empty input</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2238" 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">
2238
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<pre style="margin: 0;">+<span id="LC2238" class="line" lang="cpp"> <span class="p">}</span></span>
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2239
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<pre style="margin: 0;">+<span id="LC2239" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2240" 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">
2240
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<pre style="margin: 0;">+<span id="LC2240" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</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;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2090
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<td class="diff-line-num new_line" data-linenumber="2241" 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">
2241
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<pre style="margin: 0;"> <span id="LC2241" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Bootstrapping!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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2091
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<td class="diff-line-num new_line" data-linenumber="2242" 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">
2242
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<pre style="margin: 0;"> <span id="LC2242" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">B</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">bootstrap</span><span class="p">;</span></span>
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2092
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2243
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<pre style="margin: 0;"> <span id="LC2243" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mt19937_64</span> <span class="n" style="color: #333;">rand</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2125" 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="2276" 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">@@ -2125,6 +2276,10 @@ int main(int argc, char *argv[]) {</td>
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2125
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2276
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<pre style="margin: 0;"> <span id="LC2276" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2126" 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">
2126
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2277
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<pre style="margin: 0;"> <span id="LC2277" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2127" 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">
2127
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<td class="diff-line-num new_line" data-linenumber="2278" 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">
2278
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<pre style="margin: 0;"> <span id="LC2278" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2279" 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">
2279
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<pre style="margin: 0;">+<span id="LC2279" class="line" lang="cpp"></span>
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2280
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<pre style="margin: 0;">+<span id="LC2280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_pseudoaligned</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2281
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<pre style="margin: 0;">+<span id="LC2281" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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2282
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<pre style="margin: 0;">+<span id="LC2282" class="line" lang="cpp"> <span class="p">}</span></span>
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2128
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2283
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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="cpp"> <span class="p">}</span></span>
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2129
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2284
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<pre style="margin: 0;"> <span id="LC2284" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"pseudo"</span><span class="p">)</span> <span class="p">{</span></span>
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2130
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2285
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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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