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<h3>
Andrius Merkys 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/abea4d08d11772f3b5d6e2148f6bf6cc5baa36ac">abea4d08</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-19T01:08:32-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.48.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/-/commit/decabdf9875798d30202380be7c072678f25ad82">decabdf9</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-19T01:08:38-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.48.0+dfsg'
Update to upstream version '0.48.0+dfsg'
with Debian dir 4179b2017828b4236a6529799a5037ecde78191f</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/-/commit/fb46938064b2df7949f4011c782067f0e9cd74e8">fb469380</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-19T01:15:00-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enabling function testing.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/-/commit/d15ce76882ebbd29995fc7519387b60b6c7a105c">d15ce768</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-19T01:15:28-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build with tests depend on catch2.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/-/commit/0ac5f529fdb8c18aa6b70937abd8f7a6215c57fb">0ac5f529</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-19T01:16:00-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bumping copyright years.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/-/commit/08b062062015ec827152c6e6f4ae9d404fcffdb4">08b06206</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-19T01:18:48-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing patches, disabling Check_busOptions.seq_length_before_accessing.patch (integrated upstream).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/-/commit/651cb73e29cb626aa62f8d92ac333d8bc547b6b7">651cb73e</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-19T01:19:47-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New changelog entry.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kallisto/-/commit/1e5743ab0d054a3a530ba2322e48f4c92336b43c">1e5743ab</a></strong>
<div>
<span>by Andrius Merkys</span>
<i>at 2022-01-19T01:38:54-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Disabling tests with bustools.
</pre>
</li>
</ul>
<h4>29 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7ceee5d954a74b8640cc2bfd6c27b8fdf07d7045">
<span class="new-file">
+
.github/workflows/test.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#092e77c62ec2892b4915b2c334f2ed924f45b14e">
<span class="new-file">
+
debian/patches/disable-failing-bustools-test.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#2b96346e015f870ae988a5783c6e77e89d22871a">
debian/patches/htslib1.3
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
debian/patches/spelling
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</li>
<li class="file-stats">
<a href="#e9ffd79035f20df75689c726e3780374ee2ad4f4">
debian/patches/use_debian_packaged_htslib.patch
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
<li class="file-stats">
<a href="#ac2386b2dd6c66ed7649ace128927744f25399d5">
<span class="new-file">
+
func_tests/CMakeLists.txt
</span>
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</li>
<li class="file-stats">
<a href="#5f9e2a76725acd54d835a8d19399260cd3954c21">
<span class="new-file">
+
func_tests/runtests.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#eb8cc123f63f53de68cd814b70010244afe54ffc">
src/BUSData.cpp
</a>
</li>
<li class="file-stats">
<a href="#72660a233293b57492d69a1aca05cd0bcc23bafd">
src/BUSData.h
</a>
</li>
<li class="file-stats">
<a href="#e6d8b87f895a654f76333ff03e3e869811589fe8">
src/BUSTools.cpp
</a>
</li>
<li class="file-stats">
<a href="#436c6ee653311bc70b6cc099245981800ff0483e">
src/BUSTools.h
</a>
</li>
<li class="file-stats">
<a href="#f45107428afdf71e76b4e46fa4b37ebc79d629b3">
src/GeneModel.cpp
</a>
</li>
<li class="file-stats">
<a href="#c8778b133970078d7dc298ab3d16f53294df971d">
src/GeneModel.h
</a>
</li>
<li class="file-stats">
<a href="#6ca852079c3c5852e9a21992a760841d6ab64954">
src/Inspect.h
</a>
</li>
<li class="file-stats">
<a href="#d899a487121b0a4aa0f89fdb5446b25286dbed8e">
src/KmerIndex.cpp
</a>
</li>
<li class="file-stats">
<a href="#ef28b05af15cfcde52045cb53050e2feacc9283d">
src/KmerIndex.h
</a>
</li>
<li class="file-stats">
<a href="#9d686cfdcb10e57a7428c60a10468064ddb49a83">
src/MinCollector.cpp
</a>
</li>
<li class="file-stats">
<a href="#429cf8c697a023f342f3e4a65dded680521a6439">
src/PlaintextWriter.cpp
</a>
</li>
<li class="file-stats">
<a href="#9ab642b16309863001c06db627a92882bd233176">
src/PlaintextWriter.h
</a>
</li>
<li class="file-stats">
<a href="#04f5818132a24af33b4b06c29540101bbc992c0b">
src/ProcessReads.cpp
</a>
</li>
<li class="file-stats">
<a href="#c9d576083b226885d32fcec0ac23456a74eb4060">
src/ProcessReads.h
</a>
</li>
<li class="file-stats">
<a href="#742351309009b70e28c04c50b75d5287975926bb">
src/common.h
</a>
</li>
<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="7ceee5d954a74b8640cc2bfd6c27b8fdf07d7045">
<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#7ceee5d954a74b8640cc2bfd6c27b8fdf07d7045"><strong>.github/workflows/test.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">workflow_dispatch</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">build-linux</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build and test linux</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-18.04</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">RELEASE_OS</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">checkout branch</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@master</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Setup environment</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">id</span><span class="pi">:</span> <span class="s" style="color: #d14;">setup</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">echo ::set-output name=RELEASE_VERSION::${GITHUB_REF##*/}</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">make</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd ext/htslib && autoheader && autoconf && cd ../..</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="s" style="color: #d14;">mkdir build && cd build && cmake .. -DBUILD_FUNCTESTING=ON && make && make install && cd ..</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Setup bustools</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="s" style="color: #d14;">git clone https://github.com/BUStools/bustools.git</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd bustools && mkdir build && cd build && cmake .. && make && make install && cd ../..</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Functional testing</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd build && make test</span></span></pre>
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<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</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">@@ -74,5 +74,16 @@ if (BUILD_TESTING)</td>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>unit_tests<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>BUILD_TESTING<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>BUILD_FUNCTESTING <span class="s2" style="color: #d14;">"Build functional tests."</span> OFF<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>BUILD_FUNCTESTING<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_subdirectory</span><span class="p">(</span>func_tests<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span><span class="s2" style="color: #d14;">"Functional testing enabled."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_custom_target</span><span class="p">(</span>test</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cmake"> COMMAND /bin/bash ./func_tests/runtests.sh</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cmake"> DEPENDS ./src/kallisto</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cmake"> <span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>BUILD_FUNCTESTING<span class="p">)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cmake"></span>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># enable_testing()</span></span>
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78
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># add_test(MainTest test/tests)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kallisto (0.48.0+dfsg-1) UNRELEASED; urgency=medium</span>
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2
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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 0.48.0+dfsg</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Enabling function testing.</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Build with tests depend on catch2.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Bumping copyright years.</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Refreshing patches, disabling</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Check_busOptions.seq_length_before_accessing.patch (integrated upstream).</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andrius Merkys <merkys@debian.org> Wed, 19 Jan 2022 01:19:18 -0500</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">kallisto (0.46.2+dfsg-3) unstable; urgency=medium</span>
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2
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Team Upload.</span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#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">@@ -4,6 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> catch2,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> cmake,</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libhdf5-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libhts-dev</span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -34,6 +34,7 @@ License: public_domain.</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Copyright: 2019 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> 2022 Andrius Merkys <merkys@debian.org></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">License: BSD-2-Clause</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">License: BSD-2-Clause</span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#092e77c62ec2892b4915b2c334f2ed924f45b14e"><strong>debian/patches/disable-failing-bustools-test.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Tests fail with bustools with:</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> terminate called after throwing an instance of 'std::bad_alloc'</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> what(): std::bad_alloc</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> Aborted</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Andrius Merkys <merkys@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/func_tests/runtests.sh</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/func_tests/runtests.sh</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -257,6 +257,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> cmdexec "$kallisto quant -o $test_dir/quantlarge -t 12 -i $test_dir/basic7.idx --single -l 5 -s 2 $test_dir/large.fastq.gz $test_dir/large.fastq.gz $test_dir/large.fastq.gz $test_dir/large.fastq.gz $test_dir/large.fastq.gz"</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> checkcmdoutput "cat $test_dir/quantlarge/abundance.tsv" 024e56c50c774aa09e00a441512415aa</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "Not testing with bustools as tests fail with bustools"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+exit 0</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> ### TEST - kallisto bus ###</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span></pre>
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<li id="2b96346e015f870ae988a5783c6e77e89d22871a">
<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#2b96346e015f870ae988a5783c6e77e89d22871a"><strong>debian/patches/htslib1.3</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: Use kseq.h from htslib, not the bundled version</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">kallisto.orig</span>/src/KmerIndex.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">kallisto</span>/src/KmerIndex.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">4</span>,7 +<span class="idiff right">4</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/KmerIndex.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/KmerIndex.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">5</span>,7 +<span class="idiff right">5</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> #include <ctype.h></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> #include <zlib.h></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> #include <unordered_set></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">@@ -11,8 +11,8 @@ Subject: Use kseq.h from htslib, not the bundled version</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> #ifndef KSEQ_INIT_READY</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> #define KSEQ_INIT_READY</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">kallisto.orig</span>/src/ProcessReads.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">kallisto</span>/src/ProcessReads.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/ProcessReads.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/ProcessReads.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> /*</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> #include <zlib.h></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">@@ -30,8 +30,8 @@ Subject: Use kseq.h from htslib, not the bundled version</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> #include "PseudoBam.h"</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> #include "Fusion.hpp"</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> #include "BUSData.h"</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">kallisto.orig</span>/src/ProcessReads.h</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">kallisto</span>/src/ProcessReads.h</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/ProcessReads.h</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/ProcessReads.h</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="p">@@ -2,7 +2,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> #define KALLISTO_PROCESSREADS_H</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> </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">@@ -41,8 +41,8 @@ Subject: Use kseq.h from htslib, not the bundled version</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> #include <string></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> #include <vector></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> #include <unordered_map></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">kallisto.orig</span>/unit_tests/test_kmerhashtable.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">kallisto</span>/unit_tests/test_kmerhashtable.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/unit_tests/test_kmerhashtable.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/unit_tests/test_kmerhashtable.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> #include "KmerHashTable.h"</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_packaged_htslib.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">spelling</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">htslib1.3</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Check_busOptions.seq_length_before_accessing.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">#</span>Check_busOptions.seq_length_before_accessing.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">gcc11.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">disable-failing-bustools-test.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: fix spelling typo</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">kallisto.orig</span>/src/Inspect.h</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">kallisto</span>/src/Inspect.h</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left">49</span>,7 +2<span class="idiff right">49</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/src/Inspect.h</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/Inspect.h</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left">50</span>,7 +2<span class="idiff right">50</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> const Contig& c = index.dbGraph.contigs[i];</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> if (c.seq.size() != c.length + k-1) {</span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#e9ffd79035f20df75689c726e3780374ee2ad4f4"><strong>debian/patches/use_debian_packaged_htslib.patch</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">@@ -4,7 +4,7 @@ Description: Adapt build system to Debian packaged libhts</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/CMakeLists.txt</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">3</span>4,7 +<span class="idiff">3</span>4,7 @@</span><span class="idiff right"> ELSE(LINK MATCHES shared)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left">1</span>,7 +4<span class="idiff right">1</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> message("shared build")</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> ENDIF(LINK MATCHES static)</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </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">@@ -13,7 +13,7 @@ Description: Adapt build system to Debian packaged libhts</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> include(ExternalProject)</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> ExternalProject_Add(htslib</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -4<span class="idiff left">7</span>,7 +4<span class="idiff">7</span>,7 @@</span><span class="idiff right"> ExternalProject_Add(htslib</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">5</span>4,7 +<span class="idiff right">5</span>4,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> )</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> include_directories(${htslib_PREFIX}/src/htslib)</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">@@ -24,7 +24,7 @@ Description: Adapt build system to Debian packaged libhts</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> # add_compile_options(-Wdeprecated-register)</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -3,7 +3,9 @@</span><span class="idiff left right"> file(GLOB headers *.h *.hpp)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -3,7 +3,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> list(REMOVE_ITEM sources main.cpp)</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> </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">@@ -34,7 +34,7 @@ Description: Adapt build system to Debian packaged libhts</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> add_library(kallisto_core ${sources} ${headers})</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="p">@@ -11,7 +13,11 @@</span><span class="idiff left right"> target_include_directories(kallisto_core</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="p">@@ -11,7 +13,11 @@</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> add_executable(kallisto main.cpp)</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> find_package( Threads REQUIRED )</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">@@ -46,7 +46,7 @@ Description: Adapt build system to Debian packaged libhts</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> if(LINK MATCHES static)</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> set(BUILD_SHARED_LIBS OFF)</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">5</span>6,4 +6<span class="idiff">2</span>,4 @@</span><span class="idiff right"> else()</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left">2</span>,4 +6<span class="idiff right">8</span>,4 @@</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> endif(LINK MATCHES static)</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> </span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -5,19 +5,11 @@</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> -DLINK=shared</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># Build time test requires https://github.com/philsquared/Catch</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># -DBUILD_TESTING=ON \</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -DLINK=shared \</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -DBUILD_FUNCTESTING=1</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)</span></pre>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">#endif</span></pre>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#ac2386b2dd6c66ed7649ace128927744f25399d5"><strong>func_tests/CMakeLists.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>FuncTests<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">file</span><span class="p">(</span>COPY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/runtests.sh</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"> DESTINATION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#5f9e2a76725acd54d835a8d19399260cd3954c21"><strong>func_tests/runtests.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">### Setup ###</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">kallisto</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"./src/kallisto"</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">bustools</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"bustools"</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">test_dir</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"./func_tests"</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">cmdexec<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="nv" style="color: #008080;">expect_fail</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$2</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cmd</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cmd</span><span class="s2" style="color: #d14;"> 2> /dev/null 1> /dev/null"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$expect_fail</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"1"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"^[Failed - Returned normally but expected failure]</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"^[OK]</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> else</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$expect_fail</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"1"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"^[OK - Exited non-zero as expected]</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"^[Failed]</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">checkcmdoutput<span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"> <span class="nv" style="color: #008080;">correct_md5</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$2</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cmd</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="nv" style="color: #008080;">output_md5</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$cmd</span><span class="s2" style="color: #d14;">"</span>|md5sum|awk <span class="s1" style="color: #d14;">'{ print $1 }'</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$output_md5</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$correct_md5</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"^[Output OK]</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"^[Output incorrect! Expected: "</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$correct_md5</span><span class="s2" style="color: #d14;">"</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">" Actual: "</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$output_md5</span><span class="s2" style="color: #d14;">"</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"]</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span> </span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">### FASTA files ###</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">t1</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="s2" style="color: #d14;">ACGTGATGAGTGAGTCAGT</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="s2" style="color: #d14;">>t2</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="s2" style="color: #d14;">ACGTGATGAGATGATGAGTCAGT</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="s2" style="color: #d14;">>t3</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="s2" style="color: #d14;">ACGTGATGTGAGTCAGT</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="s2" style="color: #d14;">>t4</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="s2" style="color: #d14;">ccccaaaaaa</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="s2" style="color: #d14;">>t5</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="s2" style="color: #d14;">ttttttgggg"</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/simple.fasta</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">t1</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="s2" style="color: #d14;">AAANNNTTTKK</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="s2" style="color: #d14;">>t2</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="s2" style="color: #d14;">NNNCCCCNCCC"</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/nonATCG.fasta</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">t1</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="s2" style="color: #d14;">AAAAAAAAAAAAAAAA</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="s2" style="color: #d14;">>t2</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="s2" style="color: #d14;">CCCAAAAAAAAAAAAA</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="s2" style="color: #d14;">>t3</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="s2" style="color: #d14;">CCCGGAAAAAAAAAAA</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="s2" style="color: #d14;">>t4</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="s2" style="color: #d14;">AAAAAAAAAAAAATTT</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"><span class="s2" style="color: #d14;">>t5</span></span>
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<td class="new_line diff-line-num new" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="s2" style="color: #d14;">TAAAAAAAAAAAAAAT"</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/polyA.fasta</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">t1</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="s2" style="color: #d14;">AAATTTCCCGGGAAATTTCCCGGG</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"><span class="s2" style="color: #d14;">>t2</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"><span class="s2" style="color: #d14;">AAAtttCCCgggAAAtttCCCGGG</span></span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"><span class="s2" style="color: #d14;">>t3</span></span>
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<td class="new_line diff-line-num new" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"><span class="s2" style="color: #d14;">AAATTTCCCGGGAAATTTCCCGGG</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"><span class="s2" style="color: #d14;">>t4</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="s2" style="color: #d14;">AAATTTCCCGGGAAATTTCCCGGG</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"><span class="s2" style="color: #d14;">>t4</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"><span class="s2" style="color: #d14;">CCCCCCCCCCCCCCCCCCCCCCCC</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"><span class="s2" style="color: #d14;">>t5</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"><span class="s2" style="color: #d14;">CCCCCCCCCCCCCCCCCCCCCCCC</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" 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">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"><span class="s2" style="color: #d14;">>t5</span></span>
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<td class="new_line diff-line-num new" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"><span class="s2" style="color: #d14;">CCCCCCCCCCCCCCCCCCCCCCCC"</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/duplicates.fasta</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">### FASTQ files ###</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$test_dir</span>/simple.fasta <span class="nv" style="color: #008080;">$test_dir</span>/nonATCG.fasta <span class="nv" style="color: #008080;">$test_dir</span>/polyA.fasta <span class="nv" style="color: #008080;">$test_dir</span>/duplicates.fasta | <span class="se" style="color: #d14;">\</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{if(NR%2){ print "\@" $0 } else { printf "%s\n+\n",$0; i=0; while (i++ < length($0)) printf "J"; printf "\n" } }'</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"> | <span class="nb" style="color: #0086b3;">gzip</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/small.fastq.gz</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> /dev/null <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/medium.fastq.gz</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="o" style="font-weight: 600;">{</span>1..700<span class="o" style="font-weight: 600;">}</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do </span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$test_dir</span>/small.fastq.gz <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$test_dir</span>/medium.fastq.gz<span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> /dev/null <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/large.fastq.gz</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="o" style="font-weight: 600;">{</span>1..100<span class="o" style="font-weight: 600;">}</span><span class="p">;</span> <span class="k" style="font-weight: 600;">do </span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$test_dir</span>/medium.fastq.gz <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$test_dir</span>/large.fastq.gz<span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nv" style="color: #008080;">$test_dir</span>/medium.fastq.gz</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="shell"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Paired-end reads for basic7.idx index</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"@t1</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"><span class="s2" style="color: #d14;">ACGTGATG</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJ</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell"><span class="s2" style="color: #d14;">@t2</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell"><span class="s2" style="color: #d14;">ACGTGATG</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJ</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"><span class="s2" style="color: #d14;">@t3</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"><span class="s2" style="color: #d14;">CCCCCCCC</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJ</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell"><span class="s2" style="color: #d14;">@t4</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"><span class="s2" style="color: #d14;">ccccaaaaaa</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJJJ</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell"><span class="s2" style="color: #d14;">@t5</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"><span class="s2" style="color: #d14;">ttttttgggg</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJJJ</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">gzip</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/simple_pair1.fastq.gz</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="shell"></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"@t1</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"><span class="s2" style="color: #d14;">GAGTCAGT</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJ</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="shell"><span class="s2" style="color: #d14;">@t2</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="shell"><span class="s2" style="color: #d14;">TGAGTCAG</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJ</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="shell"><span class="s2" style="color: #d14;">@t3</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="shell"><span class="s2" style="color: #d14;">ACGTGATG</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJ</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="shell"><span class="s2" style="color: #d14;">@t4</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="shell"><span class="s2" style="color: #d14;">ccccaaaaaa</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJJJ</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="shell"><span class="s2" style="color: #d14;">@t5</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="shell"><span class="s2" style="color: #d14;">ccccaaaaaa</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJJJ</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">gzip</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/simple_pair2.fastq.gz</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Barcode+UMI FastQ file for 10Xv3</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="shell"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"@t1</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="shell"><span class="s2" style="color: #d14;">GCCCCCCCCCCCCCCGTAAAAAAAAAATGG</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ</span></span>
</pre>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="shell"><span class="s2" style="color: #d14;">@t2</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="shell"><span class="s2" style="color: #d14;">GCCCCCCCCCCCCCCGTAAAAAAAAAATGG</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ</span></span>
</pre>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="shell"><span class="s2" style="color: #d14;">@t3</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="shell"><span class="s2" style="color: #d14;">GCCCCCCCCCCCCCCGTAAAAttAAAAtGG</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ</span></span>
</pre>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="shell"><span class="s2" style="color: #d14;">@t4</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="shell"><span class="s2" style="color: #d14;">GCCCCCCggCCCCCCGtAAAAttAAAAtGG</span></span>
</pre>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ</span></span>
</pre>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="shell"><span class="s2" style="color: #d14;">@t5</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="shell"><span class="s2" style="color: #d14;">GCCCCCCttCCCCCCGtAAAAggAAAAtGG</span></span>
</pre>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="shell"><span class="s2" style="color: #d14;">+</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="shell"><span class="s2" style="color: #d14;">JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ</span></span>
</pre>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">gzip</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/10xv3.fastq.gz</span>
</pre>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="shell"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" 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="shell"><span class="c" style="color: #998; font-style: italic;">### TEST - kallisto index ###</span></span>
</pre>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="shell"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[INDEX]"</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="shell"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test k=7</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="shell"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> index -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx -k 7 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple.fasta"</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> inspect ./func_tests/basic7.idx 2>&1|head -4"</span> 356d498c030cb270a124ca06ad42a9d5</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="shell"></span>
</pre>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test k=9</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="shell"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> index -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic9.idx -k 9 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple.fasta"</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> inspect ./func_tests/basic9.idx 2>&1|head -4"</span> 9f9246d5073d8e6ba90b8644e4ed9cc9</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="shell"></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test non-ATCG bases</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" data-linenumber="193" 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">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> index -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/nonATCG.idx -k 5 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/nonATCG.fasta"</span></span>
</pre>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> inspect ./func_tests/nonATCG.idx 2>&1|head -4"</span> 5fcab956573ca37c2220d154e7760db2</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="shell"></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test polyA truncation</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> index -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/polyA.idx -k 5 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/polyA.fasta"</span></span>
</pre>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> inspect ./func_tests/polyA.idx 2>&1|head -4"</span> 8fe4f599c55a62f87e56067ccdbf865e</span>
</pre>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="shell"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test k = even number (should fail)</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="shell"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> index -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic_fail.idx -k 10 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple.fasta"</span> 1</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="shell"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test duplicate transcript names (should fail)</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="shell"></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> index -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/duplicates_fail.idx -k 11 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/duplicates.fasta"</span> 1</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="shell"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test duplicate transcript names with --make-unique</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="shell"></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> index -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/duplicates.idx -k 11 --make-unique </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/duplicates.fasta"</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> inspect ./func_tests/duplicates.idx 2>&1|head -4"</span> b57f37128e2f2e66775aa811ed994cec</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="shell"></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="shell"></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">### TEST - kallisto quant ###</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="shell"></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test single-end small.fastq.gz using various indices</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasic -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx --single -l 5 -s 2 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/small.fastq.gz"</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasic/abundance.tsv"</span> f1c8927dc29b943758242902d5c45a86</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="shell"></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantnonATCG -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/nonATCG.idx --single -l 5 -s 2 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/small.fastq.gz"</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantnonATCG/abundance.tsv"</span> 9272185ff011f9a840c29c5c40a2d390</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantpolyA -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/polyA.idx --single -l 5 -s 2 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/small.fastq.gz"</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantpolyA/abundance.tsv"</span> 745539c18d4ff07bf6de0938563f2362</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantduplicates -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/duplicates.idx --single -l 5 -s 2 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/small.fastq.gz"</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantduplicates/abundance.tsv"</span> 49a62b913a155598dd6894a2f0eb0905</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test single-end small.fastq.gz strand-specificity</span></span>
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232
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicfr -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx --single --fr-stranded -l 5 -s 2 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/small.fastq.gz"</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicfr/abundance.tsv"</span> ce2ed5a3a1bab582fcb62dc02f4d9323</span>
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235
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicrf -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx --single --rf-stranded -l 5 -s 2 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/small.fastq.gz"</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicrf/abundance.tsv"</span> 017e8ba77d7e7b39a60bb7c047e620dc</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test paired-end small.fastq.gz</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicpaired -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair1.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair2.fastq.gz"</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicpaired/abundance.tsv"</span> 1cf9cd508c04eff7cbda6e74cc1e44ea</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test paired-end small.fastq.gz with multiple pairs of files and with strand-specificity</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicpairedfr -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx --fr-stranded </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair1.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair2.fastq.gz"</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicpairedfr/abundance.tsv"</span> bc6a75291c2eb661a57b55de534dd8f0</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="shell"></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicpairedrf -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx --rf-stranded </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair1.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair2.fastq.gz"</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicpairedrf/abundance.tsv"</span> dd1ed6ed8fb393616817a3dd506f821f</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="shell"></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicpairedmultfr -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx --fr-stranded </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair1.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair2.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair2.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/simple_pair1.fastq.gz"</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantbasicpairedmultfr/abundance.tsv"</span> f810d28aed3969514f1d21120a6fc825</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test multiple large fastq files with more threads</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="shell"></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantlarge -t 12 -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx --single -l 5 -s 2 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz"</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quantlarge/abundance.tsv"</span> 024e56c50c774aa09e00a441512415aa</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="shell"></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="shell"></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">### TEST - kallisto bus ###</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="shell"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">command</span> <span class="nt" style="color: #000080;">-v</span> bustools &> /dev/null</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Error: bustools could not be found"</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="shell"></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Try custom "magic string" for -x with multiple large files and many threads</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="shell"></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> bus -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/buslarge -t 12 -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx -x 0,0,2:0,2,6:1,0,0 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz"</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$bustools</span><span class="s2" style="color: #d14;"> sort -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/buslarge/output.s.bus -t 12 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/buslarge/output.bus"</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"bustools text -p </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/buslarge/output.s.bus"</span> f3db94e1c983a1d51b8f8525bb1a5beb</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="shell"></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Try a simple 10XV3 (with unstranded pseudoalignment)</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="shell"></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> bus -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/bus10xv3 -t 1 -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx -x 10XV3 --unstranded </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/10xv3.fastq.gz </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/small.fastq.gz"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$bustools</span><span class="s2" style="color: #d14;"> sort -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/bus10xv3/output.s.bus -t 12 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/bus10xv3/output.bus"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$bustools</span><span class="s2" style="color: #d14;"> text -p </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/bus10xv3/output.s.bus"</span> f8f76f64d3ef351057f3bae016e2fa8a</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="shell"></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="shell"></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Try processing demultiplexed bulk RNA-seq with strand-specificity with EM and kallisto quant-tcc (and compare with quant) </span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="shell"></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"t1 g1</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="shell"><span class="s2" style="color: #d14;">t2 g1</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="shell"><span class="s2" style="color: #d14;">t3 g2</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="shell"><span class="s2" style="color: #d14;">t4 g2</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="shell"><span class="s2" style="color: #d14;">t5 g3"</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$test_dir</span>/t2g_test.txt <span class="c" style="color: #998; font-style: italic;"># Make a transcript-to-gene mapping file</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> bus --fr-stranded -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge -t 12 -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/basic7.idx </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/large.fastq.gz"</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$bustools</span><span class="s2" style="color: #d14;"> sort -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge/output.s.bus -t 12 </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge/output.bus"</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$bustools</span><span class="s2" style="color: #d14;"> count --cm -m -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge/counts_tcc/ -g </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/t2g_test.txt -t </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge/transcripts.txt -e </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge/matrix.ec </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge/output.bus"</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="shell">cmdexec <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$kallisto</span><span class="s2" style="color: #d14;"> quant-tcc -o </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quant_tcc_test1/ -l 5 -s 2 -i </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge/index.saved -g </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/t2g_test.txt -e </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge/counts_tcc/output.ec.txt </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/busbulklarge/counts_tcc/output.mtx"</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="shell">checkcmdoutput <span class="s2" style="color: #d14;">"cat </span><span class="nv" style="color: #008080;">$test_dir</span><span class="s2" style="color: #d14;">/quant_tcc_test1/matrix.abundance.gene.tpm.mtx"</span> ed7c7fa08e283cc6a1b136cc0e1ab039</span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#eb8cc123f63f53de68cd814b70010244afe54ffc"><strong>src/BUSData.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">@@ -50,4 +50,17 @@ std::string binaryToString(uint64_t x, size_t len) {</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">at</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="n" style="color: #333;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <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;">return</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;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<pre style="margin: 0;">+<span id="LC53" 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>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">hamming</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">^</span><span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="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;">size_t</span> <span class="n" style="color: #333;">sh</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len</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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<pre style="margin: 0;">+<span id="LC59" 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;">size_t</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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(((</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sh</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x03ULL</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="p">}</span> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">sh</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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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 class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#72660a233293b57492d69a1aca05cd0bcc23bafd"><strong>src/BUSData.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">@@ -38,4 +38,5 @@ struct BUSData {</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="nf" style="color: #900; font-weight: 600;">stringToBinary</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="p">,</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;">flag</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="nf" style="color: #900; font-weight: 600;">stringToBinary</span><span class="p">(</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="n" style="color: #333;">s</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</span><span class="p">,</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;">flag</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC40" 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="nf" style="color: #900; font-weight: 600;">binaryToString</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif // KALLISTO_BUSDATA_H</span></span></pre>
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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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">hamming</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif // KALLISTO_BUSDATA_H</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#e6d8b87f895a654f76333ff03e3e869811589fe8"><strong>src/BUSTools.cpp</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "BUS<span class="idiff left right">Data</span>.h"</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "BUS<span class="idiff left right">Tools</span>.h"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeBUSHeader</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;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bclen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">umilen</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"BUS</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -19,4 +19,28 @@ void writeBUSData(std::ofstream &out, const std::vector<BUSData> &bv) {</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">b</span><span class="p">),</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeBUSMatrix</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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="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="kt" style="color: #458; font-weight: 600;">int</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="n" style="color: #333;">data</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cols</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC26" 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;">ofstream</span> <span class="n" style="color: #333;">of</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</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;">out</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="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">writeBUSHeader</span><span class="p">(</span><span class="n" style="color: #333;">of</span><span class="p">,</span> <span class="n" style="color: #333;">BUSFORMAT_FAKE_BARCODE_LEN</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC29" 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;">data</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// reduntant </span></span>
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<pre style="margin: 0;">+<span id="LC30" 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;">size_t</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;">data</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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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">size_t</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;">v</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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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</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;">v</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">BUSData</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" 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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">UMI</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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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">ec</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;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" 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="n" style="color: #333;">v</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">b</span><span class="p">),</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <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;">of</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#436c6ee653311bc70b6cc099245981800ff0483e"><strong>src/BUSTools.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">@@ -5,7 +5,11 @@</td>
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<pre style="margin: 0;"> <span id="LC5" 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="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "BUSData.h"</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">BUSFORMAT_FAKE_BARCODE_LEN</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">;</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeBUSData</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;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">,</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BUSData</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bv</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeBUSHeader</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;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bclen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">umilen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeBUSMatrix</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC13" 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;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</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="n" style="color: #333;">data</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cols</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif // KALLISTO_BUSTOOLS_H</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#f45107428afdf71e76b4e46fa4b37ebc79d629b3"><strong>src/GeneModel.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">@@ -581,3 +581,57 @@ void Transcriptome::parseGTF(const std::string >f_fn, const KmerIndex& index,</td>
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<pre style="margin: 0;"> <span id="LC581" 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;">"Warning: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">num_trans_missing</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" transcripts were defined in GTF file, but not in the 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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<pre style="margin: 0;"> <span id="LC582" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Transcriptome</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parseGeneMap</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genemap_fn</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;">options</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC586" 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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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="n" style="color: #333;">TranscriptModel</span> <span class="n" style="color: #333;">tr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="n" style="color: #333;">tr</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp"> <span class="n" style="color: #333;">tr</span><span class="p">.</span><span class="n" style="color: #333;">chr</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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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="n" style="color: #333;">tr</span><span class="p">.</span><span class="n" style="color: #333;">gene_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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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="n" style="color: #333;">tr</span><span class="p">.</span><span class="n" style="color: #333;">strand</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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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp"> <span class="n" style="color: #333;">transcripts</span><span class="p">.</span><span class="n" style="color: #333;">push_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;">tr</span><span class="p">));</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"> <span class="n" style="color: #333;">trNameToId</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">({</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">target_names_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">i</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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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp"> </span>
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596
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<pre style="margin: 0;">+<span id="LC596" 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;">ifstream</span> <span class="n" style="color: #333;">ingenemap</span><span class="p">((</span><span class="n" style="color: #333;">genemap_fn</span><span class="p">));</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ingenemap</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" 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="n" style="color: #333;">line</span><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="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">ingenemap</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">))</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</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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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"> <span class="p">}</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" 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;">stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" 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="n" style="color: #333;">txp</span><span class="p">,</span> <span class="n" style="color: #333;">gene_name</span><span class="p">,</span> <span class="n" style="color: #333;">gene_common_name</span><span class="p">;</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" 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;">txp</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">gene_name</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">gene_common_name</span><span class="p">;</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gene_name</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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607
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<pre style="margin: 0;">+<span id="LC607" 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;">"Error: No gene associated with transcript "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">txp</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" in "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">genemap_fn</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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608
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<pre style="margin: 0;">+<span id="LC608" 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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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"> <span class="p">}</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trNameToId</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">txp</span><span class="p">);</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">trNameToId</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="n" style="color: #333;">TranscriptModel</span> <span class="n" style="color: #333;">tmodel</span><span class="p">;</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"> <span class="n" style="color: #333;">tmodel</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"> <span class="n" style="color: #333;">tmodel</span><span class="p">.</span><span class="n" style="color: #333;">length</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;">target_lens_</span><span class="p">[</span><span class="n" style="color: #333;">tmodel</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">geneNameToId</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">gene_name</span><span class="p">);</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">geneNameToId</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">GeneModel</span> <span class="n" style="color: #333;">gmodel</span><span class="p">;</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="n" style="color: #333;">gmodel</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <span class="n" style="color: #333;">gmodel</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_name</span><span class="p">;</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="n" style="color: #333;">gmodel</span><span class="p">.</span><span class="n" style="color: #333;">commonName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene_common_name</span><span class="p">;</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"> <span class="n" style="color: #333;">geneNameToId</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">({</span><span class="n" style="color: #333;">gmodel</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">gmodel</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">});</span></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">push_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;">gmodel</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="n" style="color: #333;">tmodel</span><span class="p">.</span><span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gmodel</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC624" 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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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="n" style="color: #333;">tmodel</span><span class="p">.</span><span class="n" style="color: #333;">gene_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">it2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="p">}</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">transcripts</span><span class="p">[</span><span class="n" style="color: #333;">tmodel</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">]</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">tmodel</span><span class="p">);</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" 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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629
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<pre style="margin: 0;">+<span id="LC629" 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;">"Error: Invalid transcript: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">txp</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" in "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">genemap_fn</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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630
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<pre style="margin: 0;">+<span id="LC630" 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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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC633" 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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<pre style="margin: 0;">+<span id="LC634" 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;">"Error: could not open file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">genemap_fn</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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635
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<pre style="margin: 0;">+<span id="LC635" 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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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp"> <span class="p">}</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#c8778b133970078d7dc298ab3d16f53294df971d"><strong>src/GeneModel.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">@@ -99,6 +99,7 @@ struct Transcriptome {</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">loadChromosomes</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrom_fn</span><span class="p">);</span></span>
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100
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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;">bool</span> <span class="n" style="color: #333;">translateTrPosition</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;">tr</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;">pos</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;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">TranscriptAlignment</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aln</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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101
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">parseGTF</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gtf_fn</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;">options</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">guessChromosomes</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">parseGeneMap</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">genemap_fn</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;">options</span><span class="p">);</span></span>
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102
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">addGTFLine</span><span class="p">(</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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">line</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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">guessChromosome</span><span class="p">);</span></span>
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103
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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;">void</span> <span class="n" style="color: #333;">loadTranscriptome</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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">in</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;">options</span><span class="p">);</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#6ca852079c3c5852e9a21992a760841d6ab64954"><strong>src/Inspect.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">@@ -3,6 +3,7 @@</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unordered_set></span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "KmerIndex.h"</span></span>
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<pre style="margin: 0;"> <span id="LC8" 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="LC9" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#d899a487121b0a4aa0f89fdb5446b25286dbed8e"><strong>src/KmerIndex.cpp</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "KmerIndex.h"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <random></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sstream></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <ctype.h></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <zlib.h></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unordered_set></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">@@ -782,6 +783,12 @@ bool KmerIndex::fwStep(Kmer km, Kmer& end) const {</td>
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="cpp"><span class="p">}</span></span>
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">KmerIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">load</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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">loadKmerTable</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC786" 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;">index</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">loadKmerTable</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Make an index from transcript and EC files</span></span>
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="cpp"> <span class="n" style="color: #333;">loadTranscriptsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp"> <span class="n" style="color: #333;">loadECsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="cpp"> <span class="p">}</span></span>
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="cpp"></span>
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793
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<pre style="margin: 0;"> <span id="LC793" 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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index_in</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;">index</span><span class="p">;</span></span>
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787
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794
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<pre style="margin: 0;"> <span id="LC794" 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;">ifstream</span> <span class="n" style="color: #333;">in</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">@@ -967,8 +974,73 @@ void KmerIndex::load(ProgramOptions& opt, bool loadKmerTable) {</td>
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</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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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="cpp"> </span>
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976
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="cpp"> <span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">close</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>
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978
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<pre style="margin: 0;">+<span id="LC978" 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;">ecFile</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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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="cpp"> <span class="n" style="color: #333;">loadECsFromFile</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">KmerIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">loadECsFromFile</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="p">{</span></span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="cpp"> <span class="n" style="color: #333;">ecmap</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="cpp"> <span class="n" style="color: #333;">ecmapinv</span><span class="p">.</span><span class="n" style="color: #333;">clear</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="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>
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987
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<pre style="margin: 0;">+<span id="LC987" 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;">ifstream</span> <span class="n" style="color: #333;">in</span><span class="p">((</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">ecFile</span><span class="p">));</span></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC989" 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="n" style="color: #333;">line</span><span class="p">;</span></span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">))</span> <span class="p">{</span></span>
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991
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<pre style="margin: 0;">+<span id="LC991" 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;">stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">(</span><span class="n" style="color: #333;">line</span><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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ec</span><span class="p">;</span></span>
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993
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<pre style="margin: 0;">+<span id="LC993" 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="n" style="color: #333;">transcripts</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="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">transcripts</span><span class="p">;</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">ec</span><span class="p">)</span> <span class="p">{</span></span>
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996
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<pre style="margin: 0;">+<span id="LC996" 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;">"Error: equivalence class file has a misplaced equivalence class."</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", expected "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><<</span> <span class="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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998
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<pre style="margin: 0;">+<span id="LC998" 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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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="cpp"> <span class="p">}</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" 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;">tmp_vec</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">ss2</span><span class="p">(</span><span class="n" style="color: #333;">transcripts</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="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">ss2</span><span class="p">.</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <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 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;">tmp_ecval</span><span class="p">;</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="cpp"> <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">ss2</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_ecval</span><span class="p">,</span> <span class="sc" style="color: #d14;">','</span><span class="p">);</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmp_ecval_num</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;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">tmp_ecval</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmp_ecval_num</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;">tmp_ecval_num</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">num_trans</span><span class="p">)</span> <span class="p">{</span></span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" 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;">"Error: equivalence class file has invalid value: "</span> </span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tmp_ecval</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" in "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">transcripts</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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<td class="new_line diff-line-num new" data-linenumber="1009" 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">
1009
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<pre style="margin: 0;">+<span id="LC1009" 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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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1011" 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">
1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_vec</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp_ecval_num</span><span class="p">);</span></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="cpp"> <span class="p">}</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="cpp"> <span class="n" style="color: #333;">ecmap</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp_vec</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// copy</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1014" 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">
1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="cpp"> <span class="n" style="color: #333;">ecmapinv</span><span class="p">.</span><span class="n" style="color: #333;">insert</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;">tmp_vec</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;">// move</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="cpp"> <span class="p">}</span></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" 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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1018
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<pre style="margin: 0;">+<span id="LC1018" 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;">"Error: could not open file "</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;">ecFile</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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1019
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<pre style="margin: 0;">+<span id="LC1019" 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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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp"> <span class="p">}</span></span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" 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;">"[index] number of equivalence classes loaded from file: "</span></span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pretty_num</span><span class="p">(</span><span class="n" style="color: #333;">ecmap</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;">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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970
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="cpp"><span class="p">}</span></span>
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971
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="cpp"></span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">KmerIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">loadTranscriptsFromFile</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="p">{</span></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"> <span class="n" style="color: #333;">target_names_</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <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>
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<td class="new_line diff-line-num new" data-linenumber="1028" 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">
1028
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<pre style="margin: 0;">+<span id="LC1028" 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;">ifstream</span> <span class="n" style="color: #333;">in</span><span class="p">((</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">transcriptsFile</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1029" 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">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1030" 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">
1030
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<pre style="margin: 0;">+<span id="LC1030" 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="n" style="color: #333;">txp</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1031" 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">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">txp</span><span class="p">)</span> <span class="p">{</span></span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cpp"> <span class="n" style="color: #333;">target_names_</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">txp</span><span class="p">);</span></span>
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1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1035" 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">
1035
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<pre style="margin: 0;">+<span id="LC1035" 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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1036
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<pre style="margin: 0;">+<span id="LC1036" 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;">"Error: could not open file "</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;">transcriptsFile</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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1037
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<pre style="margin: 0;">+<span id="LC1037" 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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1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="cpp"> <span class="p">}</span></span>
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1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="cpp"> <span class="n" style="color: #333;">num_trans</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="cpp"> <span class="n" style="color: #333;">target_lens_</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">num_trans</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" 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;">"[index] number of targets loaded from file: "</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pretty_num</span><span class="p">(</span><span class="n" style="color: #333;">num_trans</span><span class="p">)</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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1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"><span class="p">}</span></span>
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972
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1044
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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="cpp"></span>
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973
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1045
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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">KmerIndex</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mapPair</span><span class="p">(</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="n" style="color: #333;">s1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l1</span><span class="p">,</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="n" style="color: #333;">s2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ec</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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974
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">d1</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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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#ef28b05af15cfcde52045cb53050e2feacc9283d"><strong>src/KmerIndex.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">@@ -121,6 +121,8 @@ struct KmerIndex {</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// load methods</span></span>
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122
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">load</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="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">loadKmerTable</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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123
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">loadTranscriptSequences</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">loadECsFromFile</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>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">loadTranscriptsFromFile</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>
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124
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// positional information</span></span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#9d686cfdcb10e57a7428c60a10468064ddb49a83"><strong>src/MinCollector.cpp</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "MinCollector.h"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// utility functions</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#429cf8c697a023f342f3e4a65dded680521a6439"><strong>src/PlaintextWriter.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">@@ -64,6 +64,53 @@ void plaintext_writer(</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">plaintext_writer_gene</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC68" 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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC69" 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;">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;">targ_ids</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">alpha</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC71" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">eff_lens</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC72" 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>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> </span>
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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;">ofstream</span> <span class="n" style="color: #333;">of</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span> <span class="n" style="color: #333;">out_name</span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC78" 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;">of</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <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;">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;">"Error: Couldn't open file: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">out_name</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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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> </span>
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81
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<pre style="margin: 0;">+<span id="LC81" 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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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="p">}</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> </span>
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84
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<pre style="margin: 0;">+<span id="LC84" 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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gc</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="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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gc_tpm</span><span class="p">;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">gc</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">gc_tpm</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">tpm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counts_to_tpm</span><span class="p">(</span><span class="n" style="color: #333;">alpha</span><span class="p">,</span> <span class="n" style="color: #333;">eff_lens</span><span class="p">);</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" 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;">alpha</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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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alpha</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="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">g_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">transcripts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">gene_id</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_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 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;">gc</span><span class="p">[</span><span class="n" style="color: #333;">g_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alpha</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">gc_tpm</span><span class="p">[</span><span class="n" style="color: #333;">g_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tpm</span><span class="p">[</span><span class="n" style="color: #333;">i</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="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="p">}</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="p">}</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"gene_id"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"gene_name"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"est_counts"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"tpm"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" 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;">gc</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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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">commonName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">gc</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="sc" style="color: #d14;">'\t'</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">gc_tpm</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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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="p">}</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span><span class="p">.</span><span class="n" style="color: #333;">close</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="cpp"><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>
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67
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114
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<pre style="margin: 0;"> <span id="LC114" 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="nf" style="color: #900; font-weight: 600;">to_json</span><span class="p">(</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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">id</span><span class="p">,</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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">quote</span><span class="p">,</span></span>
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68
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">comma</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">level</span><span class="p">)</span> <span class="p">{</span></span>
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69
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="239" style="width: 35px; color: rgba(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="286" style="width: 35px; color: rgba(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">@@ -239,7 +286,7 @@ void writeFLD(const std::string &filename, const std::vector<std::pair<double, d</td>
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239
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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240
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"><span class="p">}</span></span>
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241
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeGeneList</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeGeneList</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</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 class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">writeNamesOnly</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC290" 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;">ofstream</span> <span class="n" style="color: #333;">of</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</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;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC292" 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;">of</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</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">@@ -247,7 +294,11 @@ void writeGeneList(const std::string &filename, const Transcriptome& model) {</td>
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<pre style="margin: 0;"> <span id="LC294" 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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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC296" 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;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</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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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">commonName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">writeNamesOnly</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC299" 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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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">commonName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">of</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#9ab642b16309863001c06db627a92882bd233176"><strong>src/PlaintextWriter.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">@@ -21,6 +21,14 @@ void plaintext_writer(</td>
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<pre style="margin: 0;"> <span id="LC21" 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;">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;">lens</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">plaintext_writer_gene</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC25" 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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out_name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" 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;">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;">targ_ids</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">alpha</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">eff_lens</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" 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>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC32" 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="nf" style="color: #900; font-weight: 600;">to_json</span><span class="p">(</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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">id</span><span class="p">,</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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">quote</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">comma</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">level</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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<pre style="margin: 0;"> <span id="LC34" 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">@@ -53,7 +61,10 @@ void writeECList(</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"></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;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeFLD</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</span><span class="p">,</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;">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="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flds</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeGeneList</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</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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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeGeneList</span><span class="p">(</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">filename</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 class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">writeNamesOnly</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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<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="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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">counts_to_tpm</span><span class="p">(</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">est_counts</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC67" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">eff_lens</span><span class="p">);</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="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">writeSparseBatchMatrix</span><span class="p">(</span></span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#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">@@ -26,6 +26,7 @@</td>
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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 "BUSData.h"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "BUSTools.h"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <htslib/kstring.h></span></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;">#include <unordered_set></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printVector</span><span class="p">(</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;">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;">v</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;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">o</span><span class="p">)</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">@@ -352,6 +353,23 @@ void MasterProcessor::processReads() {</td>
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352
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"> <span class="p">}</span></span>
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353
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354
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<pre style="margin: 0;"> <span id="LC354" 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;">bus_mode</span><span class="p">)</span> <span class="p">{</span></span>
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354
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355
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<pre style="margin: 0;"> <span id="LC355" 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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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">parallel_bus_read</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="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</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="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="o" style="font-weight: 600;">&&</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;">pseudobam</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parallel_bus_read</span><span class="p">)</span> <span class="p">{</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" 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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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">SR</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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360
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<pre style="margin: 0;">+<span id="LC360" 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;">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>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbatches</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="p">;</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" 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;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mutexes</span><span class="p">(</span><span class="n" style="color: #333;">nbatches</span><span class="p">);</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">parallel_bus_reader_locks</span><span class="p">.</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">mutexes</span><span class="p">);</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" 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;">nbatches</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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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">FastqSequenceReader</span> <span class="n" style="color: #333;">fSR</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">fSR</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">fSR</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">fSR</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">begin</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="n" style="color: #333;">i</span><span class="p">);</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">fSR</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">fSR</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">begin</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="p">,</span> <span class="n" style="color: #333;">fSR</span><span class="p">.</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">fSR</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="p">);</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">FSRs</span><span class="p">.</span><span class="n" style="color: #333;">push_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;">fSR</span><span class="p">));</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="p">}</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="p">}</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> </span>
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355
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373
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<pre style="margin: 0;"> <span id="LC373" 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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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</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="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="n" style="color: #333;">BUSProcessor</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span><span class="n" style="color: #333;">opt</span><span class="p">,</span><span class="n" style="color: #333;">tc</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">)));</span></span>
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<pre style="margin: 0;"> <span id="LC375" 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">@@ -375,6 +393,46 @@ void MasterProcessor::processReads() {</td>
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="p">}</span></span>
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"></span>
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"> </span>
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396
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<pre style="margin: 0;">+<span id="LC396" 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;">batch_mode</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;">batch_bus</span><span class="p">)</span> <span class="p">{</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" 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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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_ids</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;">batch_ids</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" 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="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">num_ids</span><span class="p">)</span> <span class="p">{</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO: put in thread pool</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nt</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;">min</span><span class="p">(</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="p">(</span><span class="n" style="color: #333;">num_ids</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">id</span><span class="p">));</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" 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;">pseudo_read_files_supplied</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// pseudo_read_files_supplied: read using SR (no batch identifier) rather than batchSR</span></span>
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<pre style="margin: 0;">+<span id="LC405" 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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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</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="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="n" style="color: #333;">BUSProcessor</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">tc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">)));</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="p">}</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" 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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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="p">}</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" 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="n" style="color: #333;">num_ids</span><span class="p">);</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" 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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414
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<pre style="margin: 0;">+<span id="LC414" 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;">nt</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="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</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="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="n" style="color: #333;">BUSProcessor</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">tc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">)));</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="p">}</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// let the workers do their thing</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" 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;">nt</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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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">join</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">//wait for them to finish</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="p">}</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="p">}</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="p">}</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> </span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// now handle the modification of the mincollector</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" 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;">bus_ecmap</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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426
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<pre style="margin: 0;">+<span id="LC426" 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;">u</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bus_ecmap</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ec</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;">ecmapinv</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bus_ecmapinv</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="429" 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">
429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">ec</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC430" 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;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error"</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="LC431" 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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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="p">}</span> </span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">ecmapinv</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">({</span><span class="n" style="color: #333;">u</span><span class="p">,</span><span class="n" style="color: #333;">ec</span><span class="p">});</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">ecmap</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC436" 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;">batch_mode</span><span class="p">)</span> <span class="p">{</span> </span>
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<pre style="margin: 0;"> <span id="LC437" 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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438
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_ids</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;">batch_ids</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 unfold js-unfold old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -385,13 +443,24 @@ void MasterProcessor::processReads() {</td>
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385
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nt</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;">min</span><span class="p">(</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="p">(</span><span class="n" style="color: #333;">num_ids</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">id</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">first_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" 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;">nt</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="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_bc</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">tc</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="mi" style="color: #099;">0</span><span class="p">);</span> </span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</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="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="n" style="color: #333;">ReadProcessor</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">tc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">)));</span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC393" 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;">nt</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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<pre style="margin: 0;">-<span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" 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;">pseudo_read_files_supplied</span><span class="p">)</span> <span class="p">{</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" 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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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_bc</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">tc</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="mi" style="color: #099;">0</span><span class="p">);</span> </span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</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="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="n" style="color: #333;">ReadProcessor</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">tc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="n" style="color: #333;">id</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="LC450" class="line" lang="cpp"> <span class="p">}</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" 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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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="p">}</span> </span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC455" 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="n" style="color: #333;">num_ids</span><span class="p">);</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" 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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457
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<pre style="margin: 0;">+<span id="LC457" 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;">nt</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="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_bc</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">tc</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="mi" style="color: #099;">0</span><span class="p">);</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</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="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="n" style="color: #333;">ReadProcessor</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">tc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">)));</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="p">}</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" 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;">nt</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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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC466" 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;">umi</span><span class="p">)</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">@@ -465,7 +534,7 @@ void MasterProcessor::processReads() {</td>
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ec</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;">findEC</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">ec</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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<pre style="margin: 0;">-<span id="LC468" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><span class="idiff left right">++</span></span><span class="n" style="color: #333;">tmp_counts</span><span class="p">[</span><span class="n" style="color: #333;">ec</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_counts</span><span class="p">[</span><span class="n" style="color: #333;">ec</span><span class="p">]</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">second</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC539" 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;">bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">batchCounts</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC540" 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;">tmp_counts</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -531,7 +600,7 @@ void MasterProcessor::processReads() {</td>
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<pre style="margin: 0;"> <span id="LC600" 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;">pseudobam</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp"> <span class="n" style="color: #333;">pseudobatchf_out</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC534" 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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<pre style="margin: 0;">+<span id="LC603" 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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">batch_bus</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="cpp"> <span class="n" style="color: #333;">busf_out</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC606" 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">@@ -737,7 +806,7 @@ void MasterProcessor::update(const std::vector<int>& c, const std::vector<std::v</td>
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// acquire the writer lock</span></span>
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738
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807
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<pre style="margin: 0;"> <span id="LC807" 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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">writer_lock</span><span class="p">);</span></span>
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739
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808
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="cpp"></span>
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740
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<pre style="margin: 0;">-<span id="LC740" 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;">batch_mode</span><span class="p">)</span> <span class="p">{</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" 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;">batch_mode</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">batch_bus</span></span><span class="p">)</span> <span class="p">{</span></span>
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741
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810
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<pre style="margin: 0;"> <span id="LC810" 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;">c</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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742
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="cpp"> <span class="n" style="color: #333;">tc</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 class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">c</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;">// add up ec counts</span></span>
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743
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="cpp"> <span class="n" style="color: #333;">nummapped</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="n" style="color: #333;">i</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">@@ -756,7 +825,7 @@ void MasterProcessor::update(const std::vector<int>& c, const std::vector<std::v</td>
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756
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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>
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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>
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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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759
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<pre style="margin: 0;">-<span id="LC759" 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;">batch_mode</span><span class="p">)</span> <span class="p">{</span></span>
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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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_mode</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">batch_bus</span></span><span class="p">)</span> <span class="p">{</span></span>
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829
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<pre style="margin: 0;"> <span id="LC829" 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;">u</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">newEcs</span><span class="p">)</span> <span class="p">{</span></span>
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761
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830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">newECcount</span><span class="p">[</span><span class="n" style="color: #333;">u</span><span class="p">];</span></span>
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762
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831
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<pre style="margin: 0;"> <span id="LC831" 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">@@ -829,7 +898,7 @@ void MasterProcessor::update(const std::vector<int>& c, const std::vector<std::v</td>
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829
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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="p">}</span></span>
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831
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="cpp"></span>
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832
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<pre style="margin: 0;">-<span id="LC832" 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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901
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<pre style="margin: 0;">+<span id="LC901" 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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">batch_bus</span></span><span class="p">)</span> <span class="p">{</span></span>
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833
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bus_bc_sum</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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834
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903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bus_umi_sum</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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835
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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;">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="mi" style="color: #099;">32</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="978" style="width: 35px; color: rgba(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="1047" style="width: 35px; color: rgba(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">@@ -978,7 +1047,7 @@ void ReadProcessor::operator()() {</td>
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978
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1047
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<pre style="margin: 0;"> <span id="LC1047" 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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979
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1048
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<pre style="margin: 0;"> <span id="LC1048" 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="p">;</span></span>
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980
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1049
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<pre style="margin: 0;"> <span id="LC1049" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// grab the reader lock</span></span>
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981
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<pre style="margin: 0;">-<span id="LC981" 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;">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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1050
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<pre style="margin: 0;">+<span id="LC1050" 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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_mode</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">mp</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 right">pseudo_read_files_supplied</span></span><span class="p">)</span> <span class="p">{</span></span>
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982
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1051
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<pre style="margin: 0;"> <span id="LC1051" 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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983
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1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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984
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1053
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<pre style="margin: 0;"> <span id="LC1053" 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 unfold js-unfold old_line" data-linenumber="1294" style="width: 35px; color: rgba(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="1363" style="width: 35px; color: rgba(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">@@ -1294,12 +1363,23 @@ BUSProcessor::BUSProcessor(const KmerIndex& index, const ProgramOptions& opt, co</td>
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1294
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1363
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<pre style="margin: 0;"> <span id="LC1363" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// initialize buffer</span></span>
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1295
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1364
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<pre style="margin: 0;"> <span id="LC1364" 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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1296
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1365
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<pre style="margin: 0;"> <span id="LC1365" 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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1366
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<pre style="margin: 0;">+<span id="LC1366" 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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1367
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<pre style="margin: 0;">+<span id="LC1367" 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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1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">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;">batch_files</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_files</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">reserveNfiles</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_files</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1371" 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">
1371
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<pre style="margin: 0;">+<span id="LC1371" 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;">umi</span><span class="p">)</span> <span class="p">{</span></span>
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1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">umi_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">umi_files</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">]};</span></span>
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1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1374" 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">
1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="cpp"> <span class="n" style="color: #333;">batchSR</span><span class="p">.</span><span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</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>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1376" 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">
1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="cpp"></span>
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1297
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<td class="new_line diff-line-num" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1377
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<pre style="margin: 0;"> <span id="LC1377" class="line" lang="cpp"> <span class="n" style="color: #333;">seqs</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">bufsize</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">50</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1298
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<td class="new_line diff-line-num" data-linenumber="1378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1378
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<pre style="margin: 0;"> <span id="LC1378" class="line" lang="cpp"> <span class="n" style="color: #333;">newEcs</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="old_line diff-line-num" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1299
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<td class="new_line diff-line-num" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1379
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<pre style="margin: 0;"> <span id="LC1379" class="line" lang="cpp"> <span class="n" style="color: #333;">bv</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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1300
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<td class="new_line diff-line-num" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="cpp"> <span class="n" style="color: #333;">counts</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">tc</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="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.25</span><span class="p">));</span></span>
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1301
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<td class="new_line diff-line-num old" data-linenumber="1381" 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="LC1301" 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;">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;"><span class="idiff left right">33</span></span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1302" 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">
1302
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<td class="new_line diff-line-num old" data-linenumber="1381" 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="LC1302" 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;">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;"><span class="idiff left right">33</span></span><span class="p">);</span></span>
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1381
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<pre style="margin: 0;">+<span id="LC1381" 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;">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="k" style="font-weight: 600;"><span class="idiff left">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bc_len</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1382" 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">
1382
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<pre style="margin: 0;">+<span id="LC1382" 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;">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="k" style="font-weight: 600;"><span class="idiff left">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">umi_len</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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1303
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1383
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<pre style="margin: 0;"> <span id="LC1383" class="line" lang="cpp"></span>
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1304
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1384
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<pre style="margin: 0;"> <span id="LC1384" class="line" lang="cpp"> <span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1305
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1385
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<pre style="margin: 0;"> <span id="LC1385" 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="1323" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1323,9 +1403,10 @@ BUSProcessor::BUSProcessor(BUSProcessor && o) :</td>
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1323
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1403
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<pre style="margin: 0;"> <span id="LC1403" 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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1324
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1404
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<pre style="margin: 0;"> <span id="LC1404" 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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1325
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1405
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<pre style="margin: 0;"> <span id="LC1405" class="line" lang="cpp"> <span class="n" style="color: #333;">bv</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;">bv</span><span class="p">)),</span> </span>
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1406
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<pre style="margin: 0;">+<span id="LC1406" 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>
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1326
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1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="cpp"> <span class="n" style="color: #333;">counts</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;">counts</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1327" 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">
1327
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<td class="new_line diff-line-num old" data-linenumber="1408" 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="LC1327" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bc_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</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;">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;"><span class="idiff left right">33</span></span><span class="p">);</span></span>
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1328
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<td class="new_line diff-line-num old" data-linenumber="1408" 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="LC1328" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">umi_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</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;">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;"><span class="idiff left right">33</span></span><span class="p">);</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bc_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</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;">bc_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="k" style="font-weight: 600;"><span class="idiff left">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bc_len</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1409" 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">
1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">umi_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</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;">umi_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="k" style="font-weight: 600;"><span class="idiff left">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">umi_len</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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1329
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1410
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<pre style="margin: 0;"> <span id="LC1410" 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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1330
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1411
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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">buffer</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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1331
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1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">bufsize</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="1339" style="width: 35px; color: rgba(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="1420" style="width: 35px; color: rgba(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">@@ -1339,22 +1420,42 @@ BUSProcessor::~BUSProcessor() {</td>
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1339
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1420
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<pre style="margin: 0;"> <span id="LC1420" class="line" lang="cpp"><span class="p">}</span></span>
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1340
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1421
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<pre style="margin: 0;"> <span id="LC1421" class="line" lang="cpp"></span>
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1341
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1422
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<pre style="margin: 0;"> <span id="LC1422" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BUSProcessor</span><span class="o" style="font-weight: 600;">::</span><span class="k" style="font-weight: 600;">operator</span><span class="p">()()</span> <span class="p">{</span></span>
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1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">parallel_bus_read_counter</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="new_line diff-line-num new" data-linenumber="1424" 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">
1424
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<pre style="margin: 0;">+<span id="LC1424" 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;">unordered_set</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;">parallel_bus_read_empty</span><span class="p">;</span></span>
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1342
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1425
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<pre style="margin: 0;"> <span id="LC1425" 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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1343
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1426
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<pre style="margin: 0;"> <span id="LC1426" 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="p">;</span></span>
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1427
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<pre style="margin: 0;">+<span id="LC1427" 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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1344
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1428
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<pre style="margin: 0;"> <span id="LC1428" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// grab the reader lock</span></span>
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1345
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<pre style="margin: 0;">-<span id="LC1345" class="line" lang="cpp"> <span class="p">{</span></span>
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1429
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<pre style="margin: 0;">+<span id="LC1429" 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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_mode</span> <span class="o" style="font-weight: 600;">&&</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;">pseudo_read_files_supplied</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1430" 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">
1430
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<pre style="margin: 0;">+<span id="LC1430" 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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1431
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<pre style="margin: 0;">+<span id="LC1431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1432" 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">
1432
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<pre style="margin: 0;">+<span id="LC1432" 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="new_line diff-line-num new" data-linenumber="1433" 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">
1433
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<pre style="margin: 0;">+<span id="LC1433" 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;">flags</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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1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1435" 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">
1435
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<pre style="margin: 0;">+<span id="LC1435" 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;">mp</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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">parallel_bus_read</span><span class="p">)</span> <span class="p">{</span></span>
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1436
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nbatches</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;">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;">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 class="n" style="color: #333;">nfiles</span><span class="p">;</span></span>
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1437
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<pre style="margin: 0;">+<span id="LC1437" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parallel_bus_read_counter</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">nbatches</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1438" 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">
1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parallel_bus_read_empty</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;">nbatches</span><span class="p">)</span> <span class="p">{</span></span>
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1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="cpp"> <span class="p">}</span></span>
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1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="cpp"> <span class="n" style="color: #333;">parallel_bus_read_counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1442
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<pre style="margin: 0;">+<span id="LC1442" 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;">parallel_bus_reader_locks</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<td class="new_line diff-line-num new" 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">
1443
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<pre style="margin: 0;">+<span id="LC1443" 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;">FSRs</span><span class="p">[</span><span class="n" style="color: #333;">i</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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1444
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<pre style="margin: 0;">+<span id="LC1444" class="line" lang="cpp"> <span class="n" style="color: #333;">parallel_bus_read_empty</span><span class="p">.</span><span class="n" style="color: #333;">emplace</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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1445
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<pre style="margin: 0;">+<span id="LC1445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="cpp"> <span class="p">}</span></span>
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1447
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<pre style="margin: 0;">+<span id="LC1447" class="line" lang="cpp"> <span class="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">FSRs</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">flags</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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1448
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<pre style="margin: 0;">+<span id="LC1448" 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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1346
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1449
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<pre style="margin: 0;"> <span id="LC1449" 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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1347
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1450
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<pre style="margin: 0;"> <span id="LC1450" 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><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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1348
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1451
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<pre style="margin: 0;"> <span id="LC1451" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// nothing to do</span></span>
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1349
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1452
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<pre style="margin: 0;"> <span id="LC1452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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1350
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1453
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<pre style="margin: 0;"> <span id="LC1453" 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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1351
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<td class="new_line diff-line-num" 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="c1" style="color: #998; font-style: italic;">// get new sequences</span></span>
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1352
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<pre style="margin: 0;">-<span id="LC1352" 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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1353
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<pre style="margin: 0;">-<span id="LC1353" 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><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;">flags</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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1455
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<pre style="margin: 0;">+<span id="LC1455" 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><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;">flags</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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1354
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1456
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<pre style="margin: 0;"> <span id="LC1456" class="line" lang="cpp"> <span class="p">}</span></span>
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1355
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1457
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<pre style="margin: 0;"> <span id="LC1457" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// release the reader lock</span></span>
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1356
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1458
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<pre style="margin: 0;"> <span id="LC1458" class="line" lang="cpp"> <span class="p">}</span></span>
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1357
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<pre style="margin: 0;">-<span id="LC1357" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// do the same for BUS ?!?</span></span>
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1358
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1459
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<pre style="margin: 0;"> <span id="LC1459" class="line" lang="cpp"> </span>
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1359
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<td class="new_line diff-line-num" data-linenumber="1460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1460
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<pre style="margin: 0;"> <span id="LC1460" class="line" lang="cpp"> <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;">clear</span><span class="p">();</span></span>
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1360
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<td class="new_line diff-line-num" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1461
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<pre style="margin: 0;"> <span id="LC1461" class="line" lang="cpp"> <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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1377,12 +1478,32 @@ void BUSProcessor::processBuffer() {</td>
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<pre style="margin: 0;"> <span id="LC1478" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1479" 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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1480
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<pre style="margin: 0;"> <span id="LC1480" 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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<pre style="margin: 0;">+<span id="LC1481" class="line" lang="cpp"> <span class="n" style="color: #333;">v2</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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<pre style="margin: 0;"> <span id="LC1482" 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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<pre style="margin: 0;"> <span id="LC1483" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1382" 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;">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;"><span class="idiff left right">33</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1383" 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;">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;"><span class="idiff left right">33</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1484" 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;">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="k" style="font-weight: 600;"><span class="idiff left">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bc_len</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC1485" 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;">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="k" style="font-weight: 600;"><span class="idiff left">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">umi_len</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC1486" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1487" 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="LC1488" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">bulk_like</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;">batch_bus</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">fileno</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 class="c1" style="color: #998; font-style: italic;">// Treat like bulk: no UMI</span></span>
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<pre style="margin: 0;">+<span id="LC1489" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC1490" 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;">tcount</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;">tlencount</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1491" 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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_bus</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1492" class="line" lang="cpp"> <span class="n" style="color: #333;">tcount</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;">tlencounts</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC1493" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1494" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">findFragmentLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tcount</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10000</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;">paired</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1495" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flengoal</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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1496
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<pre style="margin: 0;">+<span id="LC1496" class="line" lang="cpp"> <span class="n" style="color: #333;">flens</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1497
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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">findFragmentLength</span><span class="p">)</span> <span class="p">{</span></span>
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1498
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<pre style="margin: 0;">+<span id="LC1498" class="line" lang="cpp"> <span class="n" style="color: #333;">flengoal</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">10000</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tcount</span><span class="p">);</span></span>
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1499
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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">flengoal</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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1500
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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="cpp"> <span class="n" style="color: #333;">findFragmentLength</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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1501
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<pre style="margin: 0;">+<span id="LC1501" class="line" lang="cpp"> <span class="n" style="color: #333;">flengoal</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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1502
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<pre style="margin: 0;">+<span id="LC1502" 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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1503
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<pre style="margin: 0;">+<span id="LC1503" class="line" lang="cpp"> <span class="n" style="color: #333;">flens</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">tc</span><span class="p">.</span><span class="n" style="color: #333;">flens</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1504
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<pre style="margin: 0;">+<span id="LC1504" class="line" lang="cpp"> <span class="p">}</span></span>
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1505
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<pre style="margin: 0;">+<span id="LC1505" class="line" lang="cpp"> <span class="p">}</span></span>
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1506
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="cpp"></span>
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1507
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<pre style="margin: 0;"> <span id="LC1507" class="line" lang="cpp"> </span>
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1387
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1508
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<pre style="margin: 0;"> <span id="LC1508" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">];</span></span>
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1388
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1509
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1409" style="width: 35px; color: rgba(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">@@ -1409,6 +1530,15 @@ void BUSProcessor::processBuffer() {</td>
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1409
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1530
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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="cpp"></span>
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1410
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1531
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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">singleSeq</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;">seq</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;">1</span> <span class="p">;</span></span>
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1411
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1532
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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BUSOptionSubstr</span> <span class="n" style="color: #333;">seqopt</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;">seq</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">();</span></span>
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1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">check_tag_sequence</span> <span class="o" style="font-weight: 600;">=</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;">tagsequence</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>
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1534
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">taglen</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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1535
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">tag_binary</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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1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hamming_dist</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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1537
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_tag_sequence</span><span class="p">)</span> <span class="p">{</span></span>
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1538
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="cpp"> <span class="n" style="color: #333;">taglen</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;">tagsequence</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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1539
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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">f</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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1540
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<pre style="margin: 0;">+<span id="LC1540" class="line" lang="cpp"> <span class="n" style="color: #333;">tag_binary</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stringToBinary</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;">tagsequence</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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1541
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<pre style="margin: 0;">+<span id="LC1541" class="line" lang="cpp"> <span class="p">}</span></span>
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1412
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1542
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="cpp"></span>
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1413
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1543
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="cpp"></span>
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1414
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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;">//int incf = (bam) ? 1 : busopt.nfiles-1;</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</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">@@ -1421,42 +1551,97 @@ void BUSProcessor::processBuffer() {</td>
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1421
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1551
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<pre style="margin: 0;"> <span id="LC1551" class="line" lang="cpp"> </span>
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1422
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1552
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<pre style="margin: 0;"> <span id="LC1552" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// find where the sequence is</span></span>
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1423
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1553
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<pre style="margin: 0;"> <span id="LC1553" 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;">seq</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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1554
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<pre style="margin: 0;">+<span id="LC1554" 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;">seq2</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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1555
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<pre style="margin: 0;">+<span id="LC1555" class="line" lang="cpp"> </span>
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1556
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<pre style="margin: 0;">+<span id="LC1556" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ignore_umi</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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1557
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<pre style="margin: 0;">+<span id="LC1557" class="line" lang="cpp"> </span>
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1558
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<pre style="margin: 0;">+<span id="LC1558" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// copy the umi</span></span>
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1559
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<pre style="margin: 0;">+<span id="LC1559" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ulen</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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1560
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<pre style="margin: 0;">+<span id="LC1560" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">bad_umi</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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1561
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<pre style="margin: 0;">+<span id="LC1561" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bulk_like</span><span class="p">)</span> <span class="p">{</span></span>
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1562
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<pre style="margin: 0;">+<span id="LC1562" class="line" lang="cpp"> <span class="n" style="color: #333;">ulen</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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1563
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<pre style="margin: 0;">+<span id="LC1563" class="line" lang="cpp"> <span class="n" style="color: #333;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">;</span></span>
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1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="cpp"> <span class="n" style="color: #333;">umi</span><span class="p">[</span><span class="n" style="color: #333;">ulen</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="new_line diff-line-num new" data-linenumber="1565" 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">
1565
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<pre style="margin: 0;">+<span id="LC1565" class="line" lang="cpp"> <span class="n" style="color: #333;">ignore_umi</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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1566
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<pre style="margin: 0;">+<span id="LC1566" 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="new_line diff-line-num new" data-linenumber="1567" 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">
1567
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<pre style="margin: 0;">+<span id="LC1567" 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;">umic</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;">umi</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1568" 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">
1568
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<pre style="margin: 0;">+<span id="LC1568" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">umilen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</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;">umic</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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1569
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<pre style="margin: 0;">+<span id="LC1569" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">umilen</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">umilen</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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1570
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<pre style="margin: 0;">+<span id="LC1570" class="line" lang="cpp"> <span class="n" style="color: #333;">bad_umi</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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1571
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<pre style="margin: 0;">+<span id="LC1571" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1572
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<pre style="margin: 0;">+<span id="LC1572" class="line" lang="cpp"> <span class="p">}</span></span>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_tag_sequence</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ulen</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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1574
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<pre style="margin: 0;">+<span id="LC1574" class="line" lang="cpp"> <span class="n" style="color: #333;">umilen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">taglen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Expand to include tag sequence</span></span>
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1575
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">taglen</span><span class="p">,</span> <span class="n" style="color: #333;">umilen</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1576" 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">
1576
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<pre style="margin: 0;">+<span id="LC1576" 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="new_line diff-line-num new" data-linenumber="1577" 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">
1577
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<pre style="margin: 0;">+<span id="LC1577" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</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;">ulen</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">umic</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">umilen</span><span class="p">);</span></span>
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1578
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<pre style="margin: 0;">+<span id="LC1578" class="line" lang="cpp"> <span class="p">}</span></span>
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1579
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<pre style="margin: 0;">+<span id="LC1579" class="line" lang="cpp"> <span class="n" style="color: #333;">ulen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">umilen</span><span class="p">;</span></span>
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1580
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<pre style="margin: 0;">+<span id="LC1580" class="line" lang="cpp"> <span class="p">}</span></span>
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1581
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<pre style="margin: 0;">+<span id="LC1581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bad_umi</span><span class="p">)</span> <span class="p">{</span></span>
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1582
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<pre style="margin: 0;">+<span id="LC1582" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1583
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<pre style="margin: 0;">+<span id="LC1583" class="line" lang="cpp"> <span class="p">}</span></span>
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1584
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<pre style="margin: 0;">+<span id="LC1584" class="line" lang="cpp"> <span class="n" style="color: #333;">umi</span><span class="p">[</span><span class="n" style="color: #333;">ulen</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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1585
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<pre style="margin: 0;">+<span id="LC1585" class="line" lang="cpp"> <span class="p">}</span></span>
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1586
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<pre style="margin: 0;">+<span id="LC1586" class="line" lang="cpp"></span>
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1587
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<pre style="margin: 0;">+<span id="LC1587" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">umi_binary</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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1588
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<pre style="margin: 0;">+<span id="LC1588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_tag_sequence</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1589" 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">
1589
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<pre style="margin: 0;">+<span id="LC1589" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">f</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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1590
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<pre style="margin: 0;">+<span id="LC1590" class="line" lang="cpp"> <span class="n" style="color: #333;">umi_binary</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stringToBinary</span><span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">ulen</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1591" 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">
1591
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<pre style="margin: 0;">+<span id="LC1591" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hamming</span><span class="p">(</span><span class="n" style="color: #333;">tag_binary</span><span class="p">,</span> <span class="n" style="color: #333;">umi_binary</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="p">(</span><span class="n" style="color: #333;">ulen</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">taglen</span><span class="p">),</span> <span class="n" style="color: #333;">taglen</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">hamming_dist</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// if tag present</span></span>
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1592
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<pre style="margin: 0;">+<span id="LC1592" class="line" lang="cpp"> <span class="n" style="color: #333;">umi_binary</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">umi_binary</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">~</span><span class="p">(</span><span class="o" style="font-weight: 600;">~</span><span class="mi" style="color: #099;">0ULL</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">ulen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">taglen</span><span class="p">)));</span></span>
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1593
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<pre style="margin: 0;">+<span id="LC1593" class="line" lang="cpp"> <span class="n" style="color: #333;">ulen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ulen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">taglen</span><span class="p">;</span></span>
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1594
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<pre style="margin: 0;">+<span id="LC1594" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ulen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="p">{</span></span>
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1595
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<pre style="margin: 0;">+<span id="LC1595" class="line" lang="cpp"> <span class="n" style="color: #333;">umi_len</span><span class="p">[</span><span class="n" style="color: #333;">ulen</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1596
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<pre style="margin: 0;">+<span id="LC1596" class="line" lang="cpp"> <span class="p">}</span></span>
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1597
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<pre style="margin: 0;">+<span id="LC1597" 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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1598
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<pre style="margin: 0;">+<span id="LC1598" class="line" lang="cpp"> <span class="n" style="color: #333;">ignore_umi</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// tag not present, it's not a UMI-read</span></span>
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1599
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<pre style="margin: 0;">+<span id="LC1599" class="line" lang="cpp"> <span class="n" style="color: #333;">umi_binary</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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1600
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<pre style="margin: 0;">+<span id="LC1600" class="line" lang="cpp"> <span class="p">}</span></span>
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1601
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<pre style="margin: 0;">+<span id="LC1601" 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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1602
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<pre style="margin: 0;">+<span id="LC1602" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ulen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="p">{</span></span>
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1603
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<pre style="margin: 0;">+<span id="LC1603" class="line" lang="cpp"> <span class="n" style="color: #333;">umi_len</span><span class="p">[</span><span class="n" style="color: #333;">ulen</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1604
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<pre style="margin: 0;">+<span id="LC1604" class="line" lang="cpp"> <span class="p">}</span></span>
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1605
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<pre style="margin: 0;">+<span id="LC1605" class="line" lang="cpp"> <span class="p">}</span></span>
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1606
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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="cpp"> </span>
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1607
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<pre style="margin: 0;"> <span id="LC1607" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seqlen</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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1608
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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">seqlen2</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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1426
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1609
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<pre style="margin: 0;"> <span id="LC1609" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">singleSeq</span><span class="p">)</span> <span class="p">{</span></span>
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1427
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<pre style="margin: 0;">-<span id="LC1427" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">seqopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seqopt</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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1428
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<pre style="margin: 0;">-<span id="LC1428" class="line" lang="cpp"> <span class="n" style="color: #333;">seqlen</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;">seqopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">];</span></span>
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1610
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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ignore_umi</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">fileno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seqopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">taglen</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seqopt</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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1611
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">seqopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seqstart</span><span class="p">;</span></span>
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1612
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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="cpp"> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seqopt</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">seqopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">seqopt</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seqstart</span><span class="p">;</span></span>
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1613
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<pre style="margin: 0;">+<span id="LC1613" 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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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1614
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sopt1</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;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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1615
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<pre style="margin: 0;">+<span id="LC1615" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sopt2</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;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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1616
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<pre style="margin: 0;">+<span id="LC1616" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqstart1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ignore_umi</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">fileno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sopt1</span><span class="p">.</span><span class="n" style="color: #333;">fileno</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">taglen</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sopt1</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1617" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqstart2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ignore_umi</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">fileno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sopt2</span><span class="p">.</span><span class="n" style="color: #333;">fileno</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">taglen</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sopt2</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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1618
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<pre style="margin: 0;">+<span id="LC1618" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cplen1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sopt1</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">sopt1</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sopt1</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seqstart1</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1619" 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">
1619
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<pre style="margin: 0;">+<span id="LC1619" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cplen2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sopt2</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">sopt2</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart2</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sopt2</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seqstart2</span><span class="p">;</span></span>
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1620
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<pre style="margin: 0;">+<span id="LC1620" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">sopt1</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seqstart1</span><span class="p">;</span></span>
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1621
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<pre style="margin: 0;">+<span id="LC1621" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">sopt2</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seqstart2</span><span class="p">;</span></span>
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1622
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<pre style="margin: 0;">+<span id="LC1622" class="line" lang="cpp"> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cplen1</span><span class="p">;</span></span>
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1623
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<pre style="margin: 0;">+<span id="LC1623" class="line" lang="cpp"> <span class="n" style="color: #333;">seqlen2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cplen2</span><span class="p">;</span></span>
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1429
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1624
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<pre style="margin: 0;"> <span id="LC1624" 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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1430
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1625
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<pre style="margin: 0;"> <span id="LC1625" class="line" lang="cpp"> <span class="n" style="color: #333;">seqbuffer</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1431
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1626
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<pre style="margin: 0;"> <span id="LC1626" 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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</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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1432
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1627
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<pre style="margin: 0;"> <span id="LC1627" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sopt</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;">seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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1433
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<pre style="margin: 0;">-<span id="LC1433" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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1434
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<pre style="margin: 0;">-<span id="LC1434" class="line" lang="cpp"> <span class="n" style="color: #333;">seqbuffer</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">cplen</span><span class="p">);</span></span>
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1435
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<pre style="margin: 0;">-<span id="LC1435" class="line" lang="cpp"> <span class="n" style="color: #333;">seqbuffer</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">'N'</span><span class="p">);</span> </span>
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1628
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">ignore_umi</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">fileno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">taglen</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cplen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</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;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">seqstart</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seqstart</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1630" 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">
1630
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="cpp"> <span class="n" style="color: #333;">seqbuffer</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">sopt</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seqstart</span><span class="p">,</span> <span class="n" style="color: #333;">cplen</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1631" 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">
1631
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<pre style="margin: 0;">+<span id="LC1631" class="line" lang="cpp"> <span class="n" style="color: #333;">seqbuffer</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="sc" style="color: #d14;">'N'</span><span class="p">);</span></span>
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1436
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<td class="new_line diff-line-num" data-linenumber="1632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1632
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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="cpp"> <span class="p">}</span></span>
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1437
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<td class="new_line diff-line-num" data-linenumber="1633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1633
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<pre style="margin: 0;"> <span id="LC1633" class="line" lang="cpp"> <span class="n" style="color: #333;">seqbuffer</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" 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">
1438
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<td class="new_line diff-line-num" data-linenumber="1634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1634
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<pre style="margin: 0;"> <span id="LC1634" class="line" lang="cpp"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqbuffer</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span></span>
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1439
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1635
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="cpp"> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqbuffer</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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1440
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1636
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<pre style="margin: 0;"> <span id="LC1636" class="line" lang="cpp"> <span class="p">}</span></span>
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1441
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1637
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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="cpp"></span>
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1442
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1442" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// copy the umi</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1443" 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">
1443
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1443" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">umilen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">start</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;">umi</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</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;">umi</span><span class="p">.</span><span class="n" style="color: #333;">start</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;">umi</span><span class="p">.</span><span class="n" style="color: #333;">stop</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;">umi</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1444" 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">
1444
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1444" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</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;">umi</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">umilen</span><span class="p">)</span> <span class="p">{</span></span>
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1445
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// too short</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1446" 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">
1446
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1446" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1447" 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">
1447
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1447" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</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;">umi</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">umilen</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1448" 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">
1448
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1448" class="line" lang="cpp"> <span class="n" style="color: #333;">umi</span><span class="p">[</span><span class="n" style="color: #333;">umilen</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="old_line diff-line-num old" data-linenumber="1449" 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">
1449
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1449" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">umilen</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;">umilen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="p">{</span></span>
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1450
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1450" class="line" lang="cpp"> <span class="n" style="color: #333;">umi_len</span><span class="p">[</span><span class="n" style="color: #333;">umilen</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1451" 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">
1451
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<td class="new_line diff-line-num old" data-linenumber="1638" 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="LC1451" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1452" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1638" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// auto &bcc = busopt.bc[0];</span></span>
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<pre style="margin: 0;"> <span id="LC1640" 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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<pre style="margin: 0;"> <span id="LC1641" 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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1457
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1642
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<pre style="margin: 0;"> <span id="LC1642" 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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1458
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<pre style="margin: 0;">-<span id="LC1458" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">bcc</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">start</span></span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</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;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1459" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bclen</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1643" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">)</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;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1644" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">bcc</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bclen</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bclen</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="cpp"> <span class="n" style="color: #333;">bad_bc</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="LC1646" 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="LC1647" 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="1466" style="width: 35px; color: rgba(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">@@ -1466,6 +1651,11 @@ void BUSProcessor::processBuffer() {</td>
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<pre style="margin: 0;"> <span id="LC1651" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bad_bc</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1653" class="line" lang="cpp"> <span class="p">}</span></span>
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1654
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<pre style="margin: 0;">+<span id="LC1654" 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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_bus</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1655" class="line" lang="cpp"> <span class="n" style="color: #333;">ignore_umi</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="LC1656" class="line" lang="cpp"> <span class="n" style="color: #333;">blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BUSFORMAT_FAKE_BARCODE_LEN</span><span class="p">;</span></span>
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1657
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<pre style="margin: 0;">+<span id="LC1657" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">bc</span><span class="p">,</span> <span class="n" style="color: #333;">binaryToString</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">blen</span><span class="p">).</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">blen</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// Create fake barcode that identifies the batch</span></span>
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1658
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<pre style="margin: 0;">+<span id="LC1658" class="line" lang="cpp"> <span class="p">}</span></span>
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1469
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1659
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<pre style="margin: 0;"> <span id="LC1659" class="line" lang="cpp"> <span class="n" style="color: #333;">bc</span><span class="p">[</span><span class="n" style="color: #333;">blen</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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1470
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1660
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<pre style="margin: 0;"> <span id="LC1660" class="line" lang="cpp"></span>
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1471
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1661
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<pre style="margin: 0;"> <span id="LC1661" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">blen</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">32</span><span class="p">)</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">@@ -1483,14 +1673,74 @@ void BUSProcessor::processBuffer() {</td>
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1673
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<pre style="margin: 0;"> <span id="LC1673" class="line" lang="cpp"></span>
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1484
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1674
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<pre style="margin: 0;"> <span id="LC1674" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// process 2nd read</span></span>
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1485
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1675
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<pre style="margin: 0;"> <span id="LC1675" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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1676
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<pre style="margin: 0;">+<span id="LC1676" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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1677
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<pre style="margin: 0;">+<span id="LC1677" class="line" lang="cpp"> <span class="n" style="color: #333;">v2</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1678
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<pre style="margin: 0;">+<span id="LC1678" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">seq2</span><span class="p">,</span><span class="n" style="color: #333;">seqlen2</span><span class="p">,</span> <span class="n" style="color: #333;">v2</span><span class="p">);</span></span>
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1679
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<pre style="margin: 0;">+<span id="LC1679" class="line" lang="cpp"> <span class="p">}</span></span>
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1486
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1680
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<pre style="margin: 0;"> <span id="LC1680" class="line" lang="cpp"></span>
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1487
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1681
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<pre style="margin: 0;"> <span id="LC1681" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// collect the target information</span></span>
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1488
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1682
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<pre style="margin: 0;"> <span id="LC1682" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ec</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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1489
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<pre style="margin: 0;">-<span id="LC1489" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r</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;">intersectKmers</span><span class="p">(</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 class="nb" style="color: #0086b3;"><span class="idiff left right">false</span></span><span class="p">,</span><span class="n" style="color: #333;">u</span><span class="p">);</span></span>
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1683
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<pre style="margin: 0;">+<span id="LC1683" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r</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;">intersectKmers</span><span class="p">(</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 class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">busopt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">paired</span></span><span class="p">,</span><span class="n" style="color: #333;">u</span><span class="p">);</span></span>
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1490
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1684
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<pre style="margin: 0;"> <span id="LC1684" 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;">u</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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1491
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1685
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<pre style="margin: 0;"> <span id="LC1685" class="line" lang="cpp"> <span class="n" style="color: #333;">ec</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;">findEC</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="p">);</span></span>
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1492
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1686
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<pre style="margin: 0;"> <span id="LC1686" class="line" lang="cpp"> <span class="p">}</span></span>
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1493
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1687
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<pre style="margin: 0;"> <span id="LC1687" class="line" lang="cpp"></span>
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1688
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<pre style="margin: 0;">+<span id="LC1688" 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;">ignore_umi</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">bulk_like</span><span class="p">)</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;">strand_specific</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">u</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Strand-specificity</span></span>
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1689
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<pre style="margin: 0;">+<span id="LC1689" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">p</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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1690
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<pre style="margin: 0;">+<span id="LC1690" class="line" lang="cpp"> <span class="n" style="color: #333;">Kmer</span> <span class="n" style="color: #333;">km</span><span class="p">;</span></span>
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1691
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<pre style="margin: 0;">+<span id="LC1691" class="line" lang="cpp"> <span class="n" style="color: #333;">KmerEntry</span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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1692
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<pre style="margin: 0;">+<span id="LC1692" 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;">v</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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1693
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<pre style="margin: 0;">+<span id="LC1693" class="line" lang="cpp"> <span class="n" style="color: #333;">vtmp</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1694
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<pre style="margin: 0;">+<span id="LC1694" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">firstStrand</span> <span class="o" style="font-weight: 600;">=</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;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// FR have first read mapping forward</span></span>
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1695
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<pre style="margin: 0;">+<span id="LC1695" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findFirstMappingKmer</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">,</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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1696
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<pre style="margin: 0;">+<span id="LC1696" class="line" lang="cpp"> <span class="n" style="color: #333;">km</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Kmer</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;">p</span><span class="p">));</span></span>
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1697
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<pre style="margin: 0;">+<span id="LC1697" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">.</span><span class="n" style="color: #333;">isFw</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">km</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">km</span><span class="p">.</span><span class="n" style="color: #333;">rep</span><span class="p">()));</span> <span class="c1" style="color: #998; font-style: italic;">// k-mer maps to fw strand?</span></span>
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1698
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<pre style="margin: 0;">+<span id="LC1698" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// might need to optimize this</span></span>
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1699
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<pre style="margin: 0;">+<span id="LC1699" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c</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;">dbGraph</span><span class="p">.</span><span class="n" style="color: #333;">contigs</span><span class="p">[</span><span class="n" style="color: #333;">val</span><span class="p">.</span><span class="n" style="color: #333;">contig</span><span class="p">];</span></span>
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1700
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<pre style="margin: 0;">+<span id="LC1700" 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="n" style="color: #333;">tr</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">u</span><span class="p">)</span> <span class="p">{</span></span>
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1701
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<pre style="margin: 0;">+<span id="LC1701" 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="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">transcripts</span><span class="p">)</span> <span class="p">{</span></span>
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1702
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<pre style="margin: 0;">+<span id="LC1702" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">trid</span><span class="p">)</span> <span class="p">{</span></span>
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1703
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<pre style="margin: 0;">+<span id="LC1703" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sense</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">firstStrand</span><span class="p">)</span> <span class="p">{</span></span>
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1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// swap out </span></span>
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1705
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<pre style="margin: 0;">+<span id="LC1705" class="line" lang="cpp"> <span class="n" style="color: #333;">vtmp</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">);</span></span>
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1706
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<pre style="margin: 0;">+<span id="LC1706" class="line" lang="cpp"> <span class="p">}</span> </span>
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1707
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<pre style="margin: 0;">+<span id="LC1707" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1708
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<pre style="margin: 0;">+<span id="LC1708" class="line" lang="cpp"> <span class="p">}</span></span>
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1709
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<pre style="margin: 0;">+<span id="LC1709" class="line" lang="cpp"> <span class="p">}</span> </span>
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1710
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<pre style="margin: 0;">+<span id="LC1710" class="line" lang="cpp"> <span class="p">}</span></span>
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1711
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<pre style="margin: 0;">+<span id="LC1711" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vtmp</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;">u</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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1712
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<pre style="margin: 0;">+<span id="LC1712" class="line" lang="cpp"> <span class="n" style="color: #333;">u</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vtmp</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// copy</span></span>
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1713
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<pre style="margin: 0;">+<span id="LC1713" class="line" lang="cpp"> <span class="p">}</span></span>
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1714
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<pre style="margin: 0;">+<span id="LC1714" class="line" lang="cpp"> <span class="p">}</span></span>
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1715
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<pre style="margin: 0;">+<span id="LC1715" 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;">v2</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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1716
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<pre style="margin: 0;">+<span id="LC1716" class="line" lang="cpp"> <span class="n" style="color: #333;">vtmp</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1717
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<pre style="margin: 0;">+<span id="LC1717" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">secondStrand</span> <span class="o" style="font-weight: 600;">=</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;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RF</span><span class="p">);</span></span>
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1718
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<pre style="margin: 0;">+<span id="LC1718" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findFirstMappingKmer</span><span class="p">(</span><span class="n" style="color: #333;">v2</span><span class="p">,</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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1719
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<pre style="margin: 0;">+<span id="LC1719" class="line" lang="cpp"> <span class="n" style="color: #333;">km</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Kmer</span><span class="p">((</span><span class="n" style="color: #333;">seq2</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">p</span><span class="p">));</span></span>
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1720
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<pre style="margin: 0;">+<span id="LC1720" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">.</span><span class="n" style="color: #333;">isFw</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">km</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">km</span><span class="p">.</span><span class="n" style="color: #333;">rep</span><span class="p">()));</span> <span class="c1" style="color: #998; font-style: italic;">// k-mer maps to fw strand?</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1721" 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">
1721
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<pre style="margin: 0;">+<span id="LC1721" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// might need to optimize this</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1722" 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">
1722
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<pre style="margin: 0;">+<span id="LC1722" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c</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;">dbGraph</span><span class="p">.</span><span class="n" style="color: #333;">contigs</span><span class="p">[</span><span class="n" style="color: #333;">val</span><span class="p">.</span><span class="n" style="color: #333;">contig</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1723" 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">
1723
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<pre style="margin: 0;">+<span id="LC1723" 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="n" style="color: #333;">tr</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">u</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1724" 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">
1724
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<pre style="margin: 0;">+<span id="LC1724" 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="n" style="color: #333;">ctx</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">transcripts</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1725" 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">
1725
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">trid</span><span class="p">)</span> <span class="p">{</span></span>
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1726
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ctx</span><span class="p">.</span><span class="n" style="color: #333;">sense</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">secondStrand</span><span class="p">)</span> <span class="p">{</span></span>
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1727
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<pre style="margin: 0;">+<span id="LC1727" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// swap out </span></span>
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1728
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<pre style="margin: 0;">+<span id="LC1728" class="line" lang="cpp"> <span class="n" style="color: #333;">vtmp</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">);</span></span>
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1729
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<pre style="margin: 0;">+<span id="LC1729" class="line" lang="cpp"> <span class="p">}</span> </span>
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1730
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<pre style="margin: 0;">+<span id="LC1730" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1731
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<pre style="margin: 0;">+<span id="LC1731" class="line" lang="cpp"> <span class="p">}</span></span>
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1732
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<pre style="margin: 0;">+<span id="LC1732" class="line" lang="cpp"> <span class="p">}</span> </span>
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1733
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<pre style="margin: 0;">+<span id="LC1733" class="line" lang="cpp"> <span class="p">}</span></span>
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1734
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vtmp</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;">u</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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1735
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<pre style="margin: 0;">+<span id="LC1735" class="line" lang="cpp"> <span class="n" style="color: #333;">u</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vtmp</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// copy</span></span>
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1736
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<pre style="margin: 0;">+<span id="LC1736" class="line" lang="cpp"> <span class="p">}</span></span>
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1737
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<pre style="margin: 0;">+<span id="LC1737" class="line" lang="cpp"> <span class="p">}</span></span>
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1738
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<pre style="margin: 0;">+<span id="LC1738" class="line" lang="cpp"> <span class="n" style="color: #333;">ec</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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1739
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<pre style="margin: 0;">+<span id="LC1739" 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;">u</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// update the ec</span></span>
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1740
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<pre style="margin: 0;">+<span id="LC1740" class="line" lang="cpp"> <span class="n" style="color: #333;">ec</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;">findEC</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="p">);</span></span>
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1741
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<pre style="margin: 0;">+<span id="LC1741" class="line" lang="cpp"> <span class="p">}</span></span>
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1742
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<pre style="margin: 0;">+<span id="LC1742" class="line" lang="cpp"> <span class="p">}</span></span>
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1743
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<pre style="margin: 0;">+<span id="LC1743" class="line" lang="cpp"></span>
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1494
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1744
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<pre style="margin: 0;"> <span id="LC1744" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// find the ec</span></span>
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1495
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1745
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<pre style="margin: 0;"> <span id="LC1745" 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;">u</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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1496
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1746
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<pre style="margin: 0;"> <span id="LC1746" class="line" lang="cpp"> <span class="n" style="color: #333;">BUSData</span> <span class="n" style="color: #333;">b</span><span class="p">;</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1498" style="width: 35px; color: rgba(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="1748" style="width: 35px; color: rgba(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">@@ -1498,15 +1748,26 @@ void BUSProcessor::processBuffer() {</td>
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1498
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<pre style="margin: 0;"> <span id="LC1748" 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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1749
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<pre style="margin: 0;"> <span id="LC1749" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stringToBinary</span><span class="p">(</span><span class="n" style="color: #333;">bc</span><span class="p">,</span> <span class="n" style="color: #333;">blen</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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1500
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1750
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<pre style="margin: 0;"> <span id="LC1750" 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="n" style="color: #333;">f</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1501" class="line" lang="cpp"> <span class="n" style="color: #333;">b</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;">stringToBinary</span><span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">u<span class="idiff left right">mi</span>len</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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1751
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<pre style="margin: 0;">+<span id="LC1751" class="line" lang="cpp"> <span class="n" style="color: #333;">b</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;"><span class="idiff left">check_tag_sequence</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">bulk_like</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">umi_binary</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;">stringToBinary</span><span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">ulen</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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1752
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<pre style="margin: 0;"> <span id="LC1752" 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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1503
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1753
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<pre style="margin: 0;"> <span id="LC1753" 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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1504
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1754
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<pre style="margin: 0;"> <span id="LC1754" 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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1755
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<pre style="margin: 0;"> <span id="LC1755" 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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1506
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1756
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<pre style="margin: 0;"> <span id="LC1756" 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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1757
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<pre style="margin: 0;"> <span id="LC1757" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1508" class="line" lang="cpp"></span>
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1758
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<pre style="margin: 0;">+<span id="LC1758" class="line" lang="cpp"> </span>
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1509
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1759
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<pre style="margin: 0;"> <span id="LC1759" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//ec = tc.findEC(u);</span></span>
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1760
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<pre style="margin: 0;">+<span id="LC1760" class="line" lang="cpp"></span>
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1761
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<pre style="margin: 0;">+<span id="LC1761" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ignore_umi</span><span class="p">)</span> <span class="p">{</span></span>
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1762
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<pre style="margin: 0;">+<span id="LC1762" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">findFragmentLength</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">flengoal</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ec</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="o" style="font-weight: 600;">&&</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;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">v2</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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1763
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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// try to map the reads</span></span>
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1764
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<pre style="margin: 0;">+<span id="LC1764" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tl</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;">mapPair</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen2</span><span class="p">,</span> <span class="n" style="color: #333;">ec</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1765" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tl</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">tl</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">flens</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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1766
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<pre style="margin: 0;">+<span id="LC1766" class="line" lang="cpp"> <span class="n" style="color: #333;">flens</span><span class="p">[</span><span class="n" style="color: #333;">tl</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1767
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<pre style="margin: 0;">+<span id="LC1767" class="line" lang="cpp"> <span class="n" style="color: #333;">flengoal</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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1768
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<pre style="margin: 0;">+<span id="LC1768" class="line" lang="cpp"> <span class="p">}</span></span>
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1769
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<pre style="margin: 0;">+<span id="LC1769" class="line" lang="cpp"> <span class="p">}</span></span>
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1770
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<pre style="margin: 0;">+<span id="LC1770" class="line" lang="cpp"> <span class="p">}</span></span>
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1771
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<pre style="margin: 0;"> <span id="LC1771" class="line" lang="cpp"> </span>
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1511
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1772
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<pre style="margin: 0;"> <span id="LC1772" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// count the pseudoalignment</span></span>
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1512
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1773
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<pre style="margin: 0;"> <span id="LC1773" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ec</span> <span class="o" style="font-weight: 600;">>=</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="p">{</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -1524,16 +1785,20 @@ void BUSProcessor::processBuffer() {</td>
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1524
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1785
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<pre style="margin: 0;"> <span id="LC1785" class="line" lang="cpp"></span>
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1786
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<pre style="margin: 0;"> <span id="LC1786" 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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">pseudobam</span><span class="p">)</span> <span class="p">{</span></span>
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1526
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1787
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<pre style="margin: 0;"> <span id="LC1787" class="line" lang="cpp"> <span class="n" style="color: #333;">PseudoAlignmentInfo</span> <span class="n" style="color: #333;">info</span><span class="p">;</span></span>
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1527
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<pre style="margin: 0;">-<span id="LC1527" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1528
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<pre style="margin: 0;">-<span id="LC1528" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">false</span></span><span class="p">;</span></span>
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1788
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<pre style="margin: 0;">+<span id="LC1788" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">jmax</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1789" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">paired</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">paired</span></span><span class="p">;</span></span>
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1790
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<pre style="margin: 0;"> <span id="LC1790" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">f</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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1791
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<pre style="margin: 0;"> <span id="LC1791" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stringToBinary</span><span class="p">(</span><span class="n" style="color: #333;">bc</span><span class="p">,</span> <span class="n" style="color: #333;">blen</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1531" class="line" lang="cpp"> <span class="n" style="color: #333;">info</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;">stringToBinary</span><span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">u<span class="idiff left right">mi</span>len</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1792" class="line" lang="cpp"> <span class="n" style="color: #333;">info</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;"><span class="idiff left">check_tag_sequence</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">umi_binary</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;">stringToBinary</span><span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">,</span> <span class="n" style="color: #333;">ulen</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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1532
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1793
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<pre style="margin: 0;"> <span id="LC1793" 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;">u</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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1533
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1794
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<pre style="margin: 0;"> <span id="LC1794" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">r1empty</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;">empty</span><span class="p">();</span></span>
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1534
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1795
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<pre style="margin: 0;"> <span id="LC1795" class="line" lang="cpp"> <span class="n" style="color: #333;">KmerEntry</span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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1535
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1796
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<pre style="margin: 0;"> <span id="LC1796" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">k1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findFirstMappingKmer</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">,</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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1536
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1797
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<pre style="margin: 0;"> <span id="LC1797" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">k2pos</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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1798
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<pre style="margin: 0;">+<span id="LC1798" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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1799
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<pre style="margin: 0;">+<span id="LC1799" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">r2empty</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v2</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>
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1800
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<pre style="margin: 0;">+<span id="LC1800" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">k2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findFirstMappingKmer</span><span class="p">(</span><span class="n" style="color: #333;">v2</span><span class="p">,</span><span class="n" style="color: #333;">val</span><span class="p">);</span></span>
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1801
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<pre style="margin: 0;">+<span id="LC1801" class="line" lang="cpp"> <span class="p">}</span></span>
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1537
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1802
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<pre style="margin: 0;"> <span id="LC1802" class="line" lang="cpp"> </span>
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1538
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1803
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<pre style="margin: 0;"> <span id="LC1803" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ec</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 class="p">{</span></span>
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1539
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1804
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<pre style="margin: 0;"> <span id="LC1804" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">ec_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ec</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1670" style="width: 35px; color: rgba(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="1935" style="width: 35px; color: rgba(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">@@ -1670,7 +1935,11 @@ void AlnProcessor::operator()() {</td>
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1670
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1935
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<pre style="margin: 0;"> <span id="LC1935" 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><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;">flags</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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1671
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<td class="new_line diff-line-num" data-linenumber="1936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1936
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<pre style="margin: 0;"> <span id="LC1936" 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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1672
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1937
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<pre style="margin: 0;"> <span id="LC1937" 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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1673
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<td class="new_line diff-line-num old" data-linenumber="1938" 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="LC1673" 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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1938
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<pre style="margin: 0;">+<span id="LC1938" 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;">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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1939
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<pre style="margin: 0;">+<span id="LC1939" 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="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="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 class="n" style="color: #333;">nfiles</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// sanity checks</span></span>
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1940
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<pre style="margin: 0;">+<span id="LC1940" 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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1941
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<pre style="margin: 0;">+<span id="LC1941" 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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1942
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<pre style="margin: 0;">+<span id="LC1942" class="line" lang="cpp"> <span class="p">}</span></span>
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1943
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<pre style="margin: 0;"> <span id="LC1943" class="line" lang="cpp"> <span class="p">}</span></span>
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1944
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<pre style="margin: 0;"> <span id="LC1944" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// release the reader lock</span></span>
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1676
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1945
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<pre style="margin: 0;"> <span id="LC1945" 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="1689" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1689,7 +1958,6 @@ void AlnProcessor::operator()() {</td>
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1958
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<pre style="margin: 0;"> <span id="LC1958" class="line" lang="cpp"></span>
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1959
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<pre style="margin: 0;"> <span id="LC1959" class="line" lang="cpp"></span>
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1691
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1960
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<pre style="margin: 0;"> <span id="LC1960" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AlnProcessor</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">processBufferTrans</span><span class="p">()</span> <span class="p">{</span></span>
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1692
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<pre style="margin: 0;">-<span id="LC1692" class="line" lang="cpp"></span>
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1961
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<pre style="margin: 0;"> <span id="LC1961" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* something simple where we can construct the bam records */</span></span>
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1694
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1962
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<pre style="margin: 0;"> <span id="LC1962" 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;">bam1_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bv</span><span class="p">;</span></span>
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1963
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<pre style="margin: 0;"> <span id="LC1963" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2091" style="width: 35px; color: rgba(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="2359" style="width: 35px; color: rgba(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">@@ -2091,7 +2359,6 @@ void AlnProcessor::processBufferTrans() {</td>
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2091
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2359
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<pre style="margin: 0;"> <span id="LC2359" class="line" lang="cpp"></span>
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2360
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<pre style="margin: 0;"> <span id="LC2360" class="line" lang="cpp"></span>
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2093
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2361
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<pre style="margin: 0;"> <span id="LC2361" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">AlnProcessor</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">processBufferGenome</span><span class="p">()</span> <span class="p">{</span></span>
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2094
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<pre style="margin: 0;">-<span id="LC2094" class="line" lang="cpp"></span>
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2095
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2362
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<pre style="margin: 0;"> <span id="LC2362" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* something simple where we can construct the bam records */</span></span>
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2096
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2363
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<pre style="margin: 0;"> <span id="LC2363" 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;">bam1_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bv</span><span class="p">;</span></span>
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2097
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2364
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<pre style="margin: 0;"> <span id="LC2364" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">idnum</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="2110" style="width: 35px; color: rgba(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="2377" style="width: 35px; color: rgba(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">@@ -2110,14 +2377,21 @@ void AlnProcessor::processBufferGenome() {</td>
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2110
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<pre style="margin: 0;"> <span id="LC2377" class="line" lang="cpp"> <span class="n" style="color: #333;">genome_auxlen</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">7</span><span class="p">;</span></span>
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2378
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<pre style="margin: 0;"> <span id="LC2378" class="line" lang="cpp"> <span class="p">}</span></span>
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2379
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<pre style="margin: 0;"> <span id="LC2379" 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;">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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2113
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<pre style="margin: 0;">-<span id="LC2113" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//todo replace with what is written to busfile</span></span>
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2114
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2380
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<pre style="margin: 0;"> <span id="LC2380" class="line" lang="cpp"> <span class="n" style="color: #333;">bclen</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 class="n" style="color: #333;">getBCLength</span><span class="p">();</span></span>
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2115
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2381
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<pre style="margin: 0;"> <span id="LC2381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bclen</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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2116
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<pre style="margin: 0;">-<span id="LC2116" class="line" lang="cpp"> <span class="n" style="color: #333;">bclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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2382
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<pre style="margin: 0;">+<span id="LC2382" 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="mi" style="color: #099;">32</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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2383
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<pre style="margin: 0;">+<span id="LC2383" 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;">bus_bc_len</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="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">bus_bc_len</span><span class="p">[</span><span class="n" style="color: #333;">bclen</span><span class="p">])</span> <span class="p">{</span></span>
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2384
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<pre style="margin: 0;">+<span id="LC2384" class="line" lang="cpp"> <span class="n" style="color: #333;">bclen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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2385
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<pre style="margin: 0;">+<span id="LC2385" class="line" lang="cpp"> <span class="p">}</span></span>
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2386
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<pre style="margin: 0;">+<span id="LC2386" class="line" lang="cpp"> <span class="p">}</span></span>
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2387
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<pre style="margin: 0;"> <span id="LC2387" class="line" lang="cpp"> <span class="p">}</span></span>
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2388
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<pre style="margin: 0;"> <span id="LC2388" class="line" lang="cpp"> <span class="n" style="color: #333;">umilen</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 class="n" style="color: #333;">getUMILength</span><span class="p">();</span></span>
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2119
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2389
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<pre style="margin: 0;"> <span id="LC2389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">umilen</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="LC2120" class="line" lang="cpp"> <span class="n" style="color: #333;">umilen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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2390
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<pre style="margin: 0;">+<span id="LC2390" 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="mi" style="color: #099;">32</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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<pre style="margin: 0;">+<span id="LC2391" 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;">bus_umi_len</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="n" style="color: #333;">mp</span><span class="p">.</span><span class="n" style="color: #333;">bus_umi_len</span><span class="p">[</span><span class="n" style="color: #333;">umilen</span><span class="p">])</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2392" class="line" lang="cpp"> <span class="n" style="color: #333;">umilen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2393" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2394" class="line" lang="cpp"> <span class="p">}</span></span>
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2395
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<pre style="margin: 0;"> <span id="LC2395" class="line" lang="cpp"> <span class="p">}</span></span>
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2396
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<pre style="margin: 0;"> <span id="LC2396" class="line" lang="cpp"></span>
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2123
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2397
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<pre style="margin: 0;"> <span id="LC2397" class="line" lang="cpp"> <span class="n" style="color: #333;">genome_auxlen</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">bclen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">umilen</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2129,28 +2403,31 @@ void AlnProcessor::processBufferGenome() {</td>
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2129
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2403
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<pre style="margin: 0;"> <span id="LC2403" class="line" lang="cpp"> <span class="n" style="color: #333;">KmerEntry</span> <span class="n" style="color: #333;">val1</span><span class="p">,</span> <span class="n" style="color: #333;">val2</span><span class="p">;</span></span>
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2130
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2404
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<pre style="margin: 0;"> <span id="LC2404" 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;">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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2131
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2405
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<pre style="margin: 0;"> <span id="LC2405" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</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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2406
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<pre style="margin: 0;">+<span id="LC2406" 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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="cpp"> <span class="n" style="color: #333;">paired</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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2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="cpp"> <span class="p">}</span></span>
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2132
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2409
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<pre style="margin: 0;"> <span id="LC2409" class="line" lang="cpp"> <span class="p">}</span></span>
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2133
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<pre style="margin: 0;">-<span id="LC2133" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">readpaired</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">||</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;">bus_mode</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 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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2134
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<pre style="margin: 0;">-<span id="LC2134" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC2135" class="line" lang="cpp"> </span>
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2136
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2410
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<pre style="margin: 0;"> <span id="LC2410" class="line" lang="cpp"></span>
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2137
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2411
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<pre style="margin: 0;"> <span id="LC2411" 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;">n</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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2138
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2412
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<pre style="margin: 0;"> <span id="LC2412" class="line" lang="cpp"> <span class="n" style="color: #333;">bam1_t</span> <span class="n" style="color: #333;">b1</span><span class="p">,</span><span class="n" style="color: #333;">b2</span><span class="p">,</span> <span class="n" style="color: #333;">b1c</span><span class="p">,</span> <span class="n" style="color: #333;">b2c</span><span class="p">;</span></span>
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2139
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<pre style="margin: 0;">-<span id="LC2139" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">si1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">readpaired</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;">i</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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2140
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<pre style="margin: 0;">-<span id="LC2140" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">si2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">readpaired</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;">i</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2141
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<pre style="margin: 0;">-<span id="LC2141" class="line" lang="cpp"> </span>
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2413
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<pre style="margin: 0;">+<span id="LC2413" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">si1</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2414" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">si2</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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</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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<pre style="margin: 0;">+<span id="LC2415" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// For BUS file processing with paired-end reads:</span></span>
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2416
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<pre style="margin: 0;">+<span id="LC2416" 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;">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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2417
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<pre style="margin: 0;">+<span id="LC2417" 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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2418
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<pre style="margin: 0;">+<span id="LC2418" class="line" lang="cpp"> <span class="n" style="color: #333;">si1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">fileno</span><span class="p">;</span></span>
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2419
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<pre style="margin: 0;">+<span id="LC2419" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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2420
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<pre style="margin: 0;">+<span id="LC2420" class="line" lang="cpp"> <span class="n" style="color: #333;">si2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">fileno</span><span class="p">;</span></span>
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2421
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<pre style="margin: 0;">+<span id="LC2421" class="line" lang="cpp"> <span class="p">}</span></span>
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2422
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<pre style="margin: 0;">+<span id="LC2422" class="line" lang="cpp"> <span class="p">}</span></span>
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2423
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<pre style="margin: 0;"> <span id="LC2423" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rlen1</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;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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2143
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2424
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<pre style="margin: 0;"> <span id="LC2424" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rlen2</span><span class="p">;</span></span>
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2144
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<pre style="margin: 0;">-<span id="LC2144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">readpaired</span><span class="p">)</span> <span class="p">{</span></span>
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2425
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<pre style="margin: 0;">+<span id="LC2425" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq1_offset</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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2426
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<pre style="margin: 0;">+<span id="LC2426" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq2_offset</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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2427
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<pre style="margin: 0;">+<span id="LC2427" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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2145
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2428
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<pre style="margin: 0;"> <span id="LC2428" class="line" lang="cpp"> <span class="n" style="color: #333;">rlen2</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;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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2146
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2429
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<pre style="margin: 0;"> <span id="LC2429" class="line" lang="cpp"> <span class="p">}</span></span>
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2147
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2430
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<pre style="margin: 0;"> <span id="LC2430" class="line" lang="cpp"> </span>
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2148
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<pre style="margin: 0;">-<span id="LC2148" 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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">().</span><span class="n" style="color: #333;">fileno</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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2149
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<pre style="margin: 0;">-<span id="LC2149" 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;">swap</span><span class="p">(</span><span class="n" style="color: #333;">si1</span><span class="p">,</span><span class="n" style="color: #333;">si2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2150" 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;">swap</span><span class="p">(</span><span class="n" style="color: #333;">rlen1</span><span class="p">,</span><span class="n" style="color: #333;">rlen2</span><span class="p">);</span></span>
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2151
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<pre style="margin: 0;">-<span id="LC2151" class="line" lang="cpp"> <span class="p">}</span></span>
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2152
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<pre style="margin: 0;">-<span id="LC2152" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC2153" class="line" lang="cpp"></span>
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2154
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<pre style="margin: 0;"> <span id="LC2431" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fill in the bam core info</span></span>
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2432
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<pre style="margin: 0;"> <span id="LC2432" class="line" lang="cpp"> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</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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2433
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<pre style="margin: 0;"> <span id="LC2433" class="line" lang="cpp"> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2176,16 +2453,42 @@ void AlnProcessor::processBufferGenome() {</td>
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<pre style="margin: 0;"> <span id="LC2453" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2454" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC2455" class="line" lang="cpp"> <span class="n" style="color: #333;">PseudoAlignmentInfo</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pi</span> <span class="o" style="font-weight: 600;">=</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;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC2179" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2180" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fill in the data info</span></span>
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2181
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<pre style="margin: 0;">-<span id="LC2181" class="line" lang="cpp"> <span class="n" style="color: #333;">fillBamRecord</span><span class="p">(</span><span class="n" style="color: #333;">b1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r1empty</span><span class="p">,</span> <span class="n" style="color: #333;">genome_auxlen</span><span class="p">);</span></span>
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2182
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<pre style="margin: 0;">-<span id="LC2182" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//b1.id = idnum++;</span></span>
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<pre style="margin: 0;">-<span id="LC2183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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2184
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<pre style="margin: 0;">-<span id="LC2184" class="line" lang="cpp"> <span class="n" style="color: #333;">fillBamRecord</span><span class="p">(</span><span class="n" style="color: #333;">b2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r2empty</span><span class="p">,</span> <span class="n" style="color: #333;">genome_auxlen</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC2185" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// b2.id = idnum++;</span></span>
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2186
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<pre style="margin: 0;">-<span id="LC2186" class="line" lang="cpp"> <span class="p">}</span></span>
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2187
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<pre style="margin: 0;"> <span id="LC2456" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC2188" 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;">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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<pre style="margin: 0;">+<span id="LC2457" 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;">mp</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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2458
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<pre style="margin: 0;">+<span id="LC2458" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fill in the data info</span></span>
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<pre style="margin: 0;">+<span id="LC2459" class="line" lang="cpp"> <span class="n" style="color: #333;">fillBamRecord</span><span class="p">(</span><span class="n" style="color: #333;">b1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r1empty</span><span class="p">,</span> <span class="n" style="color: #333;">genome_auxlen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2460" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//b1.id = idnum++;</span></span>
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2461
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<pre style="margin: 0;">+<span id="LC2461" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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2462
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<pre style="margin: 0;">+<span id="LC2462" class="line" lang="cpp"> <span class="n" style="color: #333;">fillBamRecord</span><span class="p">(</span><span class="n" style="color: #333;">b2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r2empty</span><span class="p">,</span> <span class="n" style="color: #333;">genome_auxlen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2463" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// b2.id = idnum++;</span></span>
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2464
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<pre style="margin: 0;">+<span id="LC2464" class="line" lang="cpp"> <span class="p">}</span></span>
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2465
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<pre style="margin: 0;">+<span id="LC2465" class="line" lang="cpp"> <span class="p">}</span></span>
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2466
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<pre style="margin: 0;">+<span id="LC2466" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2467
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<pre style="margin: 0;">+<span id="LC2467" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">tag_present</span> <span class="o" style="font-weight: 600;">=</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;">tagsequence</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">UMI</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 class="c1" style="color: #998; font-style: italic;">// tag+UMI present in the sequence</span></span>
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2468
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<pre style="margin: 0;">+<span id="LC2468" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">umi_first_file</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 class="n" style="color: #333;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">fileno</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 class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">fileno</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// UMI-containing file is the first file (file number 0)</span></span>
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<pre style="margin: 0;">+<span id="LC2469" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tagseqstart</span><span class="p">;</span></span>
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2470
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<pre style="margin: 0;">+<span id="LC2470" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tag_present</span><span class="p">)</span> <span class="p">{</span></span>
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2471
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<pre style="margin: 0;">+<span id="LC2471" class="line" lang="cpp"> <span class="n" style="color: #333;">tagseqstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">umi_first_file</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 class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">start</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 class="n" style="color: #333;">seq</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Position where the actual sequence begins when tag+UMI present</span></span>
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2472
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<pre style="margin: 0;">+<span id="LC2472" class="line" lang="cpp"> <span class="p">}</span></span>
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2473
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<pre style="margin: 0;">+<span id="LC2473" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC2474" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fill in the data info</span></span>
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<pre style="margin: 0;">+<span id="LC2475" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tag_present</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">umi_first_file</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2476" class="line" lang="cpp"> <span class="n" style="color: #333;">rlen1</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;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">tagseqstart</span><span class="p">;</span></span>
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2477
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<pre style="margin: 0;">+<span id="LC2477" class="line" lang="cpp"> <span class="n" style="color: #333;">seq1_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tagseqstart</span><span class="p">;</span></span>
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2478
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<pre style="margin: 0;">+<span id="LC2478" class="line" lang="cpp"> <span class="n" style="color: #333;">fillBamRecord</span><span class="p">(</span><span class="n" style="color: #333;">b1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tagseqstart</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tagseqstart</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">tagseqstart</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r1empty</span><span class="p">,</span> <span class="n" style="color: #333;">genome_auxlen</span><span class="p">);</span></span>
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2479
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<pre style="margin: 0;">+<span id="LC2479" 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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2480
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<pre style="margin: 0;">+<span id="LC2480" class="line" lang="cpp"> <span class="n" style="color: #333;">fillBamRecord</span><span class="p">(</span><span class="n" style="color: #333;">b1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r1empty</span><span class="p">,</span> <span class="n" style="color: #333;">genome_auxlen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2481" class="line" lang="cpp"> <span class="p">}</span></span>
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2482
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<pre style="margin: 0;">+<span id="LC2482" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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2483
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<pre style="margin: 0;">+<span id="LC2483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tag_present</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">umi_first_file</span><span class="p">)</span> <span class="p">{</span></span>
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2484
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<pre style="margin: 0;">+<span id="LC2484" class="line" lang="cpp"> <span class="n" style="color: #333;">rlen2</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;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">tagseqstart</span><span class="p">;</span></span>
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2485
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<pre style="margin: 0;">+<span id="LC2485" class="line" lang="cpp"> <span class="n" style="color: #333;">seq2_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tagseqstart</span><span class="p">;</span></span>
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2486
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<pre style="margin: 0;">+<span id="LC2486" class="line" lang="cpp"> <span class="n" style="color: #333;">fillBamRecord</span><span class="p">(</span><span class="n" style="color: #333;">b2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tagseqstart</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tagseqstart</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">tagseqstart</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r2empty</span><span class="p">,</span> <span class="n" style="color: #333;">genome_auxlen</span><span class="p">);</span></span>
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2487
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<pre style="margin: 0;">+<span id="LC2487" 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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2488
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<pre style="margin: 0;">+<span id="LC2488" class="line" lang="cpp"> <span class="n" style="color: #333;">fillBamRecord</span><span class="p">(</span><span class="n" style="color: #333;">b2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r2empty</span><span class="p">,</span> <span class="n" style="color: #333;">genome_auxlen</span><span class="p">);</span></span>
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2489
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<pre style="margin: 0;">+<span id="LC2489" class="line" lang="cpp"> <span class="p">}</span></span>
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2490
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<pre style="margin: 0;">+<span id="LC2490" class="line" lang="cpp"> <span class="p">}</span></span>
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2491
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<pre style="margin: 0;">+<span id="LC2491" class="line" lang="cpp"></span>
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2189
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2492
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<pre style="margin: 0;"> <span id="LC2492" class="line" lang="cpp"> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">;</span></span>
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2190
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2493
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<pre style="margin: 0;"> <span id="LC2493" class="line" lang="cpp"> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">l_data</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="sc" style="color: #d14;">'R'</span><span class="p">;</span></span>
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2191
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2494
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<pre style="margin: 0;"> <span id="LC2494" class="line" lang="cpp"> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">l_data</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="sc" style="color: #d14;">'Z'</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2196" style="width: 35px; color: rgba(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">@@ -2196,9 +2499,25 @@ void AlnProcessor::processBufferGenome() {</td>
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2196
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2499
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<pre style="margin: 0;"> <span id="LC2499" class="line" lang="cpp"> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'U'</span><span class="p">;</span></span>
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2197
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2500
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<pre style="margin: 0;"> <span id="LC2500" class="line" lang="cpp"> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">l_data</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="sc" style="color: #d14;">'R'</span><span class="p">;</span></span>
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2198
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2501
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<pre style="margin: 0;"> <span id="LC2501" class="line" lang="cpp"> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">l_data</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="sc" style="color: #d14;">'Z'</span><span class="p">;</span></span>
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2199
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<pre style="margin: 0;">-<span id="LC2199" 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;">binaryToString</span><span class="p">(</span><span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">UMI</span><span class="p">,</span> <span class="n" style="color: #333;">umilen</span><span class="p">);</span></span>
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2502
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<pre style="margin: 0;">+<span id="LC2502" 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;">mp</span><span class="p">.</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">tagsequence</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">UMI</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 class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Non-UMI read</span></span>
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2503
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<pre style="margin: 0;">+<span id="LC2503" 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;">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;">umilen</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">);</span></span>
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2504
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<pre style="margin: 0;">+<span id="LC2504" 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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2505
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<pre style="margin: 0;">+<span id="LC2505" 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;">binaryToString</span><span class="p">(</span><span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">UMI</span><span class="p">,</span> <span class="n" style="color: #333;">umilen</span><span class="p">);</span></span>
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2506
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<pre style="margin: 0;">+<span id="LC2506" class="line" lang="cpp"> <span class="p">}</span></span>
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2200
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2507
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<pre style="margin: 0;"> <span id="LC2507" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">umilen</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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2201
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<td class="new_line diff-line-num" data-linenumber="2508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2508
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<pre style="margin: 0;"> <span id="LC2508" class="line" lang="cpp"> <span class="n" style="color: #333;">b1</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">umilen</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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2509
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<pre style="margin: 0;">+<span id="LC2509" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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2510
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<pre style="margin: 0;">+<span id="LC2510" class="line" lang="cpp"> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">;</span></span>
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2511
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<pre style="margin: 0;">+<span id="LC2511" class="line" lang="cpp"> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</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="sc" style="color: #d14;">'R'</span><span class="p">;</span></span>
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2512
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<pre style="margin: 0;">+<span id="LC2512" class="line" lang="cpp"> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</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="sc" style="color: #d14;">'Z'</span><span class="p">;</span></span>
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2513
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<pre style="margin: 0;">+<span id="LC2513" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">bc</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">bclen</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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2514
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<pre style="margin: 0;">+<span id="LC2514" class="line" lang="cpp"> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">bclen</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="new_line diff-line-num new" data-linenumber="2515" 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">
2515
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<pre style="margin: 0;">+<span id="LC2515" class="line" lang="cpp"> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'U'</span><span class="p">;</span></span>
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2516
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<pre style="margin: 0;">+<span id="LC2516" class="line" lang="cpp"> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</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="sc" style="color: #d14;">'R'</span><span class="p">;</span></span>
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2517
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<pre style="margin: 0;">+<span id="LC2517" class="line" lang="cpp"> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</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="sc" style="color: #d14;">'Z'</span><span class="p">;</span></span>
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2518
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<pre style="margin: 0;">+<span id="LC2518" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">umilen</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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2519
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<pre style="margin: 0;">+<span id="LC2519" class="line" lang="cpp"> <span class="n" style="color: #333;">b2</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">umilen</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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2520
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<pre style="margin: 0;">+<span id="LC2520" class="line" lang="cpp"> <span class="p">}</span></span>
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2202
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2521
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<pre style="margin: 0;"> <span id="LC2521" class="line" lang="cpp"> <span class="p">}</span></span>
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2203
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2522
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<pre style="margin: 0;"> <span id="LC2522" class="line" lang="cpp"></span>
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2204
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2523
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<pre style="margin: 0;"> <span id="LC2523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r1empty</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r2empty</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="2334" style="width: 35px; color: rgba(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="2653" style="width: 35px; color: rgba(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">@@ -2334,11 +2653,11 @@ void AlnProcessor::processBufferGenome() {</td>
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2334
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2653
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<pre style="margin: 0;"> <span id="LC2653" 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;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">strInfo1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">},</span> <span class="n" style="color: #333;">strInfo2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">};</span></span>
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2335
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2654
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<pre style="margin: 0;"> <span id="LC2654" class="line" lang="cpp"> </span>
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2336
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2655
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<pre style="margin: 0;"> <span id="LC2655" 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;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r1empty</span><span class="p">)</span> <span class="p">{</span></span>
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2337
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<pre style="margin: 0;">-<span id="LC2337" class="line" lang="cpp"> <span class="n" style="color: #333;">km1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Kmer</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">k1pos</span><span class="p">);</span></span>
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2656
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<pre style="margin: 0;">+<span id="LC2656" class="line" lang="cpp"> <span class="n" style="color: #333;">km1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Kmer</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si1</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left">seq1_offset</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;">pi</span><span class="p">.</span><span class="n" style="color: #333;">k1pos</span><span class="p">);</span></span>
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2338
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2657
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<pre style="margin: 0;"> <span id="LC2657" class="line" lang="cpp"> <span class="n" style="color: #333;">strInfo1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strandednessInfo</span><span class="p">(</span><span class="n" style="color: #333;">km1</span><span class="p">,</span> <span class="n" style="color: #333;">val1</span><span class="p">,</span> <span class="n" style="color: #333;">ua</span><span class="p">);</span></span>
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2339
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2658
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<pre style="margin: 0;"> <span id="LC2658" class="line" lang="cpp"> <span class="p">}</span></span>
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2340
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2659
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<pre style="margin: 0;"> <span id="LC2659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r2empty</span><span class="p">)</span> <span class="p">{</span></span>
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2341
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<pre style="margin: 0;">-<span id="LC2341" class="line" lang="cpp"> <span class="n" style="color: #333;">km2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Kmer</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pi</span><span class="p">.</span><span class="n" style="color: #333;">k2pos</span><span class="p">);</span></span>
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2660
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<pre style="margin: 0;">+<span id="LC2660" class="line" lang="cpp"> <span class="n" style="color: #333;">km2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Kmer</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">[</span><span class="n" style="color: #333;">si2</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left">seq2_offset</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;">pi</span><span class="p">.</span><span class="n" style="color: #333;">k2pos</span><span class="p">);</span></span>
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2342
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2661
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<pre style="margin: 0;"> <span id="LC2661" class="line" lang="cpp"> <span class="n" style="color: #333;">strInfo2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strandednessInfo</span><span class="p">(</span><span class="n" style="color: #333;">km2</span><span class="p">,</span> <span class="n" style="color: #333;">val2</span><span class="p">,</span> <span class="n" style="color: #333;">ua</span><span class="p">);</span></span>
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2343
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2662
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<pre style="margin: 0;"> <span id="LC2662" class="line" lang="cpp"> <span class="p">}</span></span>
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2663
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<pre style="margin: 0;"> <span id="LC2663" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2459" style="width: 35px; color: rgba(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">@@ -2459,7 +2778,7 @@ void AlnProcessor::processBufferGenome() {</td>
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2778
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<pre style="margin: 0;"> <span id="LC2778" class="line" lang="cpp"> <span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="p">;</span></span>
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2460
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2779
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<pre style="margin: 0;"> <span id="LC2779" 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;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r1empty</span><span class="p">)</span> <span class="p">{</span></span>
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2461
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2780
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<pre style="margin: 0;"> <span id="LC2780" class="line" lang="cpp"> <span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">.</span><span class="n" style="color: #333;">chrpos</span><span class="p">;</span></span>
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2462
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<td class="new_line diff-line-num old" data-linenumber="2781" 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="LC2462" class="line" lang="cpp"> <span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_reg2bin</span><span class="p">(</span><span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">);</span></span>
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2781
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<pre style="margin: 0;">+<span id="LC2781" class="line" lang="cpp"> <span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_reg2bin</span><span class="p">(</span><span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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;">si1</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;"><span class="idiff left">seq1_offset</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-</span></span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">);</span></span>
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2463
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2782
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<pre style="margin: 0;"> <span id="LC2782" class="line" lang="cpp"> <span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">255</span><span class="p">;</span></span>
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2783
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<pre style="margin: 0;"> <span id="LC2783" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">useEM</span><span class="p">)</span> <span class="p">{</span></span>
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2784
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<pre style="margin: 0;"> <span id="LC2784" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b1c</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// set ZW tag</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2789" style="width: 35px; color: rgba(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">@@ -2470,7 +2789,7 @@ void AlnProcessor::processBufferGenome() {</td>
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2470
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2789
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<pre style="margin: 0;"> <span id="LC2789" class="line" lang="cpp"> <span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">chr</span><span class="p">;</span></span>
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2471
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2790
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<pre style="margin: 0;"> <span id="LC2790" 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;">pi</span><span class="p">.</span><span class="n" style="color: #333;">r2empty</span><span class="p">)</span> <span class="p">{</span></span>
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2472
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2791
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<pre style="margin: 0;"> <span id="LC2791" class="line" lang="cpp"> <span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tra</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">chrpos</span><span class="p">;</span></span>
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2473
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<td class="new_line diff-line-num old" data-linenumber="2792" 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="LC2473" class="line" lang="cpp"> <span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_reg2bin</span><span class="p">(</span><span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">);</span></span>
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2792
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<pre style="margin: 0;">+<span id="LC2792" class="line" lang="cpp"> <span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">bin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_reg2bin</span><span class="p">(</span><span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</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;">si2</span><span class="p">].</span><span class="n" style="color: #333;">second</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="n" style="color: #333;"><span class="idiff right">seq2_offset</span></span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">);</span></span>
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2474
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2793
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<pre style="margin: 0;"> <span id="LC2793" class="line" lang="cpp"> <span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">255</span><span class="p">;</span></span>
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2475
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2794
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<pre style="margin: 0;"> <span id="LC2794" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">useEM</span><span class="p">)</span> <span class="p">{</span></span>
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2476
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2795
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<pre style="margin: 0;"> <span id="LC2795" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b2c</span><span class="p">.</span><span class="n" style="color: #333;">l_data</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2914" style="width: 35px; color: rgba(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="3233" style="width: 35px; color: rgba(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">@@ -2914,7 +3233,7 @@ bool FastqSequenceReader::fetchSequences(char *buf, const int limit, std::vector</td>
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2914
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3233
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<pre style="margin: 0;"> <span id="LC3233" class="line" lang="cpp"> <span class="p">}</span></span>
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2915
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3234
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<pre style="margin: 0;"> <span id="LC3234" class="line" lang="cpp"></span>
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2916
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3235
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<pre style="margin: 0;"> <span id="LC3235" class="line" lang="cpp"> <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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2917
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<pre style="margin: 0;">-<span id="LC2917" 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="p">);</span></span>
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3236
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<pre style="margin: 0;">+<span id="LC3236" 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 class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>
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2918
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3237
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<pre style="margin: 0;"> <span id="LC3237" 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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2919
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3238
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<pre style="margin: 0;"> <span id="LC3238" 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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2920
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3239
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<pre style="margin: 0;"> <span id="LC3239" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#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">@@ -179,8 +179,6 @@ public:</td>
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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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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"></span>
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181
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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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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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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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184
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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;">batchCounts</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_ids</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="p">{});</span></span>
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185
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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;">tlencounts</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_ids</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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186
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">batchFlens</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_ids</span><span class="p">.</span><span class="n" style="color: #333;">size</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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="mi" style="color: #099;">1000</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 unfold js-unfold old_line" data-linenumber="198" style="width: 35px; color: rgba(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="196" style="width: 35px; color: rgba(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">@@ -198,10 +196,16 @@ public:</td>
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198
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196
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<pre style="margin: 0;"> <span id="LC196" 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;">pseudobam</span><span class="p">)</span> <span class="p">{</span></span>
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199
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp"> <span class="n" style="color: #333;">pseudobatchf_out</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;">out</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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200
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="p">}</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" 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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199
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<pre style="margin: 0;">+<span id="LC199" 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="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_bus</span><span class="p">)</span> <span class="p">{</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" 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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">bus_bc_len</span><span class="p">));</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" 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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">bus_umi_len</span><span class="p">));</span></span>
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202
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="n" style="color: #333;">busf_out</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;">"/output.bus"</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;">out</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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203
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> </span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">writeBUSHeader</span><span class="p">(</span><span class="n" style="color: #333;">busf_out</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 class="n" style="color: #333;">getBCLength</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 class="n" style="color: #333;">getUMILength</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC204" 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_bus</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">writeBUSHeader</span><span class="p">(</span><span class="n" style="color: #333;">busf_out</span><span class="p">,</span> <span class="n" style="color: #333;">BUSFORMAT_FAKE_BARCODE_LEN</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC206" 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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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">writeBUSHeader</span><span class="p">(</span><span class="n" style="color: #333;">busf_out</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 class="n" style="color: #333;">getBCLength</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 class="n" style="color: #333;">getUMILength</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="227" style="width: 35px; color: rgba(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">@@ -227,10 +231,13 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="p">}</span></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="LC233" 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="LC234" 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;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parallel_bus_reader_locks</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">parallel_bus_read</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC236" 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="LC237" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC239" 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;">SR</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC240" 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;">FastqSequenceReader</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">FSRs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC241" 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="LC242" 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="LC243" 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">@@ -335,6 +342,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC342" 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="LC343" 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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<pre style="margin: 0;"> <span id="LC344" 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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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">FastqSequenceReader</span> <span class="n" style="color: #333;">batchSR</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bc_len</span><span class="p">[</span><span class="mi" style="color: #099;">33</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">umi_len</span><span class="p">[</span><span class="mi" style="color: #099;">33</span><span class="p">];</span></span>
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<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#742351309009b70e28c04c50b75d5287975926bb"><strong>src/common.h</strong></a>
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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 "0.4<span class="idiff left right">6.2</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 "0.4<span class="idiff left right">8.0</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,9 +22,11 @@ struct BUSOptionSubstr {</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">BUSOptions</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nfiles</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"> <span class="n" style="color: #333;">BUSOptionSubstr</span> <span class="n" style="color: #333;">umi</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;">BUSOptionSubstr</span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span> <span class="n" style="color: #333;">umi</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC26" 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;">BUSOptionSubstr</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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<pre style="margin: 0;"> <span id="LC27" 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;">BUSOptionSubstr</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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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">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="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">getBCLength</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="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">@@ -32,6 +34,8 @@ struct BUSOptions {</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <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;">b</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bc</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <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;">b</span><span class="p">.</span><span class="n" style="color: #333;">stop</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="LC38" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <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">@@ -41,11 +45,19 @@ struct BUSOptions {</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">getUMILength</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">umi</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <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;">umi</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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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <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;">u</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">umi</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">u</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</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="c"> <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;">u</span><span class="p">.</span><span class="n" style="color: #333;">stop</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="LC54" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">u</span><span class="p">.</span><span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">u</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,6 +76,7 @@ struct ProgramOptions {</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bootstrap</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC77" 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;">transfasta</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">batch_mode</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">pseudo_read_files_supplied</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC80" 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="LC81" 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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82
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<pre style="margin: 0;"> <span id="LC82" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -87,6 +100,8 @@ struct ProgramOptions {</td>
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87
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">StrandType</span> <span class="p">{</span><span class="n" style="color: #333;">None</span><span class="p">,</span> <span class="n" style="color: #333;">FR</span><span class="p">,</span> <span class="n" style="color: #333;">RF</span><span class="p">};</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">StrandType</span> <span class="n" style="color: #333;">strand</span><span class="p">;</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">umi</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">batch_bus_write</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">batch_bus</span><span class="p">;</span></span>
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90
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105
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<pre style="margin: 0;"> <span id="LC105" 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;">gfa</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// used for inspect</span></span>
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91
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">inspect_thorough</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">single_overhang</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">@@ -94,6 +109,12 @@ struct ProgramOptions {</td>
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109
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<pre style="margin: 0;"> <span id="LC109" 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;">chromFile</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="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;">bedFile</span><span class="p">;</span></span>
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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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">technology</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tagsequence</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;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tccFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC114" 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;">ecFile</span><span class="p">;</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" 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;">fldFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC116" 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;">transcriptsFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC117" 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;">genemap</span><span class="p">;</span></span>
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97
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"></span>
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98
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"><span class="n" style="color: #333;">ProgramOptions</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span></span>
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99
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">verbose</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="128" style="width: 35px; color: rgba(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 +128,7 @@ ProgramOptions() :</td>
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107
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">min_range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">),</span></span>
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<td class="old_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">bootstrap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<td class="old_line diff-line-num" 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">
109
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130
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<pre style="margin: 0;"> <span id="LC130" 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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<td class="old_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="131" 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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">pseudo_read_files_supplied</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<td class="old_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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132
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<pre style="margin: 0;"> <span id="LC132" 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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<td class="old_line diff-line-num" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
111
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133
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<pre style="margin: 0;"> <span id="LC133" 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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<td class="old_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
112
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134
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<pre style="margin: 0;"> <span id="LC134" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" style="width: 35px; color: rgba(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="145" style="width: 35px; color: rgba(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">@@ -123,6 +145,8 @@ ProgramOptions() :</td>
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123
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">fusion</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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124
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<td class="new_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">strand</span><span class="p">(</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">None</span><span class="p">),</span></span>
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125
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="n" style="color: #333;">umi</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">batch_bus_write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">batch_bus</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<td class="old_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
126
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<td class="new_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"> <span class="n" style="color: #333;">inspect_thorough</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<td class="old_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
127
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<td class="new_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"> <span class="n" style="color: #333;">single_overhang</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span></span>
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128
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> <span class="p">{}</span></span>
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<li id="b958235ee8db37bcaceda04b6d55553b450c2db4">
<a href="https://salsa.debian.org/med-team/kallisto/-/compare/a1ccc5194630a474877de4bad34ce53508312a1c...1e5743ab0d054a3a530ba2322e48f4c92336b43c#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">@@ -8,6 +8,7 @@</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <thread></span></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <time.h></span></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>
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12
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<td class="new_line diff-line-num" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdio></span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" 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">@@ -379,23 +380,118 @@ void ParseOptionsEMOnly(int argc, char **argv, ProgramOptions& opt) {</td>
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379
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"> <span class="p">}</span></span>
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"><span class="p">}</span></span>
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ParseOptionsTCCQuant</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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384
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<pre style="margin: 0;">+<span id="LC384" 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;">"o:i:T:e:f:l:s:t:g:G:b:d:"</span><span class="p">;</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">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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386
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<pre style="margin: 0;">+<span id="LC386" 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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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"txnames"</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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388
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<pre style="margin: 0;">+<span id="LC388" 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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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fragment-file"</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;">'f'</span><span class="p">},</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fragment-length"</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;">'l'</span><span class="p">},</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"sd"</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;">'s'</span><span class="p">},</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" 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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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"ec-file"</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;">'e'</span><span class="p">},</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"genemap"</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;">'g'</span><span class="p">},</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"gtf"</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;">'G'</span><span class="p">},</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bootstrap-samples"</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;">'b'</span><span class="p">},</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"seed"</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;">'d'</span><span class="p">},</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" 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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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"> <span class="p">};</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">option_index</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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402
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<pre style="margin: 0;">+<span id="LC402" 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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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">,</span><span class="n" style="color: #333;">opt_string</span><span class="p">,</span> <span class="n" style="color: #333;">long_options</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">option_index</span><span class="p">);</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> </span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</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 class="p">{</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="p">}</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> </span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">:</span> <span class="p">{</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" 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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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="p">}</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">:</span> <span class="p">{</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" 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;">fldFile</span><span class="p">;</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">:</span> <span class="p">{</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" 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;">fld</span><span class="p">;</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="p">}</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">:</span> <span class="p">{</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" 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;">sd</span><span class="p">;</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="p">}</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">:</span> <span class="p">{</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" 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="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="p">}</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">:</span> <span class="p">{</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="p">}</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">:</span> <span class="p">{</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">ecFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="p">}</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">:</span> <span class="p">{</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">genemap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">:</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">gtfFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC446" 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="LC447" class="line" lang="cpp"> <span class="p">}</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" 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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449
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<pre style="margin: 0;">+<span id="LC449" 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;">bootstrap</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC450" 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="LC451" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'d'</span><span class="p">:</span> <span class="p">{</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" 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;">seed</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC454" 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="LC455" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'T'</span><span class="p">:</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">transcriptsFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="p">}</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" 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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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="p">}</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" 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="n" style="color: #333;">optind</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;">argc</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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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <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;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC466" 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;">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="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="LC467" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">tccFile</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="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ParseOptionsPseudo</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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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose_flag</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="LC473" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">single_flag</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="LC474" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand_flag</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="LC475" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand_FR_flag</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="LC476" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand_RF_flag</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="LC477" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pbam_flag</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="LC478" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gbam_flag</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="LC479" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">umi_flag</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="LC480" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">quant_flag</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="LC481" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bus_flag</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="LC482" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC391" 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;">"t:i:l:s:o:b:u:g:"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC483" 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;">"t:i:l:s:o:b:u:g:<span class="idiff left right">n</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">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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<pre style="margin: 0;"> <span id="LC485" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// long args</span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">verbose_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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395
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"single"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">single_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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396
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//{"strand-specific", no_argument, &strand_flag, 1},</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fr-stranded"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strand_FR_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"rf-stranded"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strand_RF_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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397
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"pseudobam"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pbam_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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398
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"quant"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">quant_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"bus"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bus_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" 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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399
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"umi"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">umi_flag</span><span class="p">,</span> <span class="sc" style="color: #d14;">'u'</span><span class="p">},</span></span>
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400
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"batch"</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;">'b'</span><span class="p">},</span></span>
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401
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// short args</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="435" style="width: 35px; color: rgba(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="531" style="width: 35px; color: rgba(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">@@ -435,6 +531,10 @@ void ParseOptionsPseudo(int argc, char **argv, ProgramOptions& opt) {</td>
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435
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531
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<pre style="margin: 0;"> <span id="LC531" 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;">sd</span><span class="p">;</span></span>
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436
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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437
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="p">}</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" 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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535
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<pre style="margin: 0;">+<span id="LC535" 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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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="p">}</span></span>
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438
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">:</span> <span class="p">{</span></span>
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439
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539
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<pre style="margin: 0;"> <span id="LC539" 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="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</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">@@ -456,6 +556,14 @@ void ParseOptionsPseudo(int argc, char **argv, ProgramOptions& opt) {</td>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">umi</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="LC557" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">single_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// UMI implies single-end reads</span></span>
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="cpp"> <span class="p">}</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bus_flag</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC561" 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;">num</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_bus_write</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="LC563" 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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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_bus</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="LC565" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// all other arguments are fast[a/q] files to be read</span></span>
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<pre style="margin: 0;"> <span id="LC569" 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="n" style="color: #333;">optind</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;">argc</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -478,6 +586,16 @@ void ParseOptionsPseudo(int argc, char **argv, ProgramOptions& opt) {</td>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand_flag</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</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="LC588" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand_FR_flag</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</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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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;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"> <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>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand_RF_flag</span><span class="p">)</span> <span class="p">{</span></span>
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596
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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;">strand_specific</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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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RF</span><span class="p">;</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="p">}</span></span>
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481
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="cpp"></span>
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482
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600
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pbam_flag</span><span class="p">)</span> <span class="p">{</span></span>
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483
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601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp"> <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="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="532" style="width: 35px; color: rgba(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="650" style="width: 35px; color: rgba(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">@@ -532,6 +650,8 @@ void ListSingleCellTechnologies() {</td>
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532
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650
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"10xv1 10x 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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533
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651
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"10xv2 10x 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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534
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652
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"10xv3 10x 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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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Bulk Bulk RNA-seq or Smart-seq2 (multiplexed)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"BDWTA BD Rhapsody WTA"</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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655
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<pre style="margin: 0;"> <span id="LC655" 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>
</pre>
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536
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656
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<pre style="margin: 0;"> <span id="LC656" 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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537
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657
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<pre style="margin: 0;"> <span id="LC657" 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>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="539" style="width: 35px; color: rgba(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="659" style="width: 35px; color: rgba(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">@@ -539,27 +659,40 @@ void ListSingleCellTechnologies() {</td>
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539
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659
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<pre style="margin: 0;"> <span id="LC659" 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>
</pre>
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<td class="old_line diff-line-num" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
540
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<td class="new_line diff-line-num" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
660
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<pre style="margin: 0;"> <span id="LC660" 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>
</pre>
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<pre style="margin: 0;"> <span id="LC661" 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>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SmartSeq3 Smart-seq3"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SPLiT-seq SPLiT-seq"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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664
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<pre style="margin: 0;"> <span id="LC664" 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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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Visium 10x Visium Spatial Transcriptomics"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC666" 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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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC669" 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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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose_flag</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="LC671" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gbam_flag</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="LC672" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">paired_end_flag</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="LC673" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand_FR_flag</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="LC674" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand_RF_flag</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="LC675" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unstranded_flag</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="LC676" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC550" 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:lbng:c:"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC677" 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:lbng:c:<span class="idiff left right">T:B:</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">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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<pre style="margin: 0;"> <span id="LC679" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">verbose_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC680" 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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681
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<pre style="margin: 0;"> <span id="LC681" 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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682
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<pre style="margin: 0;"> <span id="LC682" 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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683
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<pre style="margin: 0;"> <span id="LC683" 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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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"batch"</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;">'B'</span><span class="p">},</span></span>
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685
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<pre style="margin: 0;"> <span id="LC685" 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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558
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686
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<pre style="margin: 0;"> <span id="LC686" 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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687
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<pre style="margin: 0;"> <span id="LC687" 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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688
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"genomebam"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gbam_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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689
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"gtf"</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;">'g'</span><span class="p">},</span></span>
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562
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690
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"chromosomes"</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;">'c'</span><span class="p">},</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"tag"</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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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"fr-stranded"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strand_FR_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"rf-stranded"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strand_RF_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"unstranded"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">unstranded_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"paired"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">paired_end_flag</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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696
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<pre style="margin: 0;"> <span id="LC696" 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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697
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp"> <span class="p">};</span></span>
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="601" style="width: 35px; color: rgba(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="734" style="width: 35px; color: rgba(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">@@ -601,6 +734,11 @@ void ParseOptionsBus(int argc, char **argv, ProgramOptions& opt) {</td>
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601
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734
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<pre style="margin: 0;"> <span id="LC734" 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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602
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735
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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603
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736
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="cpp"> <span class="p">}</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" 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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<td class="new_line diff-line-num new" data-linenumber="738" 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">
738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_mode</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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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="741" 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">
741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"> <span class="p">}</span></span>
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604
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742
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<pre style="margin: 0;"> <span id="LC742" 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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605
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743
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<pre style="margin: 0;"> <span id="LC743" 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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606
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744
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="613" style="width: 35px; color: rgba(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="751" style="width: 35px; color: rgba(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">@@ -613,6 +751,10 @@ void ParseOptionsBus(int argc, char **argv, ProgramOptions& opt) {</td>
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613
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751
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<pre style="margin: 0;"> <span id="LC751" 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;">chromFile</span><span class="p">;</span></span>
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614
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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615
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="cpp"> <span class="p">}</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'T'</span><span class="p">:</span> <span class="p">{</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" 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;">tagsequence</span><span class="p">;</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="cpp"> <span class="p">}</span></span>
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616
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758
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<pre style="margin: 0;"> <span id="LC758" 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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617
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="cpp"> <span class="p">}</span></span>
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618
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760
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<pre style="margin: 0;"> <span id="LC760" 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="631" style="width: 35px; color: rgba(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="773" style="width: 35px; color: rgba(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">@@ -631,6 +773,26 @@ void ParseOptionsBus(int argc, char **argv, ProgramOptions& opt) {</td>
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631
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">genomebam</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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632
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand_FR_flag</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</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="LC778" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="cpp"> <span class="p">}</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand_RF_flag</span><span class="p">)</span> <span class="p">{</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</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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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RF</span><span class="p">;</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="cpp"> <span class="p">}</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="cpp"> </span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unstranded_flag</span><span class="p">)</span> <span class="p">{</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</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="LC788" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">None</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="cpp"> <span class="p">}</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">paired_end_flag</span><span class="p">)</span> <span class="p">{</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">single_end</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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793
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<pre style="margin: 0;">+<span id="LC793" 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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<pre style="margin: 0;">+<span id="LC794" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">single_end</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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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="cpp"> <span class="p">}</span></span>
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// all other arguments are fast[a/q] files to be read</span></span>
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<pre style="margin: 0;"> <span id="LC798" 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="n" style="color: #333;">optind</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;">argc</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -726,11 +888,7 @@ bool ParseTechnology(const std::string &techstr, BUSOptions& busopt, std::vector</td>
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="cpp"> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: empty UMI list "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">umistr</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="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</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="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="cpp"> <span class="n" style="color: #333;">errorList</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: only a single UMI list allow "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">umistr</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC731" 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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<pre style="margin: 0;">-<span id="LC732" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC733" 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;">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;">v</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">());</span></span>
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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;">umi</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;">move</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC894" 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;">convert_commas_to_vector</span><span class="p">(</span><span class="n" style="color: #333;">seqstr</span><span class="p">,</span> <span class="n" style="color: #333;">v</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="808" style="width: 35px; color: rgba(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">@@ -808,7 +966,7 @@ bool CheckOptionsBus(ProgramOptions& opt) {</td>
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="cpp"></span>
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check files</span></span>
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<pre style="margin: 0;">-<span id="LC811" 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;">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="mi" style="color: #099;">0</span><span class="p">)</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="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;">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="mi" style="color: #099;">0</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><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 right">batch_mode</span></span><span class="p">)</span> <span class="p">{</span></span>
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812
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970
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<pre style="margin: 0;"> <span id="LC970" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Missing read files"</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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813
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<pre style="margin: 0;"> <span id="LC971" 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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972
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<pre style="margin: 0;"> <span id="LC972" 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">@@ -853,67 +1011,264 @@ bool CheckOptionsBus(ProgramOptions& opt) {</td>
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853
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", but only "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" cores on the machine"</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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854
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1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="cpp"> <span class="p">}</span> </span>
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855
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="cpp"> <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>
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857
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<pre style="margin: 0;">-<span id="LC857" 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="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Error: need to specify technology to use"</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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1014
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<pre style="margin: 0;">+<span id="LC1014" 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;">technology</span><span class="p">.</span><span class="n" style="color: #333;">empty</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;">batch_mode</span><span class="p">)</span> <span class="p">{</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" 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: cannot specify both -x and --batch"</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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859
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1016
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<pre style="margin: 0;"> <span id="LC1016" 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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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="cpp"> <span class="p">}</span></span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="cpp"></span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp"> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">None</span><span class="p">;</span></span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp"></span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" 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="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// kallisto pseudo</span></span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" 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;">num</span><span class="p">)</span> <span class="p">{</span></span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_bus_write</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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1024
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<pre style="margin: 0;">+<span id="LC1024" 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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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_bus</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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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1027" 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">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check for read files</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1028" 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">
1028
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<pre style="margin: 0;">+<span id="LC1028" 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;">batch_mode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1029" 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">
1029
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<pre style="margin: 0;">+<span id="LC1029" 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;">"[bus] no technology specified; will try running read files as-is"</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="new_line diff-line-num new" data-linenumber="1030" 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">
1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_mode</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="new_line diff-line-num new" data-linenumber="1031" 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">
1031
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<pre style="margin: 0;">+<span id="LC1031" 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;">single_end</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="mi" style="color: #099;">2</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="new_line diff-line-num new" data-linenumber="1032" 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">
1032
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<pre style="margin: 0;">+<span id="LC1032" 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: paired-end mode requires an even number of input files"</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="new_line diff-line-num new" data-linenumber="1033" 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">
1033
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<pre style="margin: 0;">+<span id="LC1033" 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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<td class="new_line diff-line-num new" data-linenumber="1034" 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">
1034
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<pre style="margin: 0;">+<span id="LC1034" 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="new_line diff-line-num new" data-linenumber="1035" 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">
1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="cpp"> <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>
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<td class="new_line diff-line-num new" data-linenumber="1036" 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">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sample_id</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="new_line diff-line-num new" data-linenumber="1037" 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">
1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</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;">files</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1038" 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">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_ids</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"batch"</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;">sample_id</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1039" 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">
1039
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<pre style="margin: 0;">+<span id="LC1039" 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="n" style="color: #333;">f1</span><span class="p">,</span><span class="n" style="color: #333;">f2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1040" 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">
1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1041" 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">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="cpp"> <span class="n" style="color: #333;">f1</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;">i</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1042" 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">
1042
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<pre style="margin: 0;">+<span id="LC1042" 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;">single_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1043" 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">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">f1</span><span class="p">});</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1044" 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">
1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1045" 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">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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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1046
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<pre style="margin: 0;">+<span id="LC1046" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">f1</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="new_line diff-line-num new" data-linenumber="1047" 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">
1047
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<pre style="margin: 0;">+<span id="LC1047" 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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<td class="new_line diff-line-num new" data-linenumber="1048" 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">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1049" 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">
1049
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<pre style="margin: 0;">+<span id="LC1049" 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="new_line diff-line-num new" data-linenumber="1050" 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">
1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1051" 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">
1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">f2</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;">i</span><span class="p">];</span></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">f1</span><span class="p">,</span><span class="n" style="color: #333;">f2</span><span class="p">});</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1053" 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">
1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1054" 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">
1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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="new_line diff-line-num new" data-linenumber="1055" 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">
1055
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<pre style="margin: 0;">+<span id="LC1055" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">f1</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="new_line diff-line-num new" data-linenumber="1056" 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">
1056
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<pre style="margin: 0;">+<span id="LC1056" 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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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1058" 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">
1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="cpp"> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1059" 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">
1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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="new_line diff-line-num new" data-linenumber="1060" 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">
1060
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<pre style="margin: 0;">+<span id="LC1060" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">f2</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="new_line diff-line-num new" data-linenumber="1061" 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">
1061
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<pre style="margin: 0;">+<span id="LC1061" 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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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="cpp"> <span class="p">}</span></span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="cpp"> <span class="p">}</span></span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="cpp"> <span class="n" style="color: #333;">sample_id</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="cpp"> <span class="p">}</span></span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample_id</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="new_line diff-line-num new" data-linenumber="1068" 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">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">pseudo_read_files_supplied</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Only one sample supplied; use SR instead of batchSR to read</span></span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"> <span class="p">}</span></span>
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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1071" 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">
1071
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<pre style="margin: 0;">+<span id="LC1071" 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;">ret</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1072" 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">
1072
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<pre style="margin: 0;">+<span id="LC1072" 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;">"[bus] no technology specified; will try running read files supplied in batch file"</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="new_line diff-line-num new" data-linenumber="1073" 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">
1073
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<pre style="margin: 0;">+<span id="LC1073" 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;">single_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1074" 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">
1074
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<pre style="margin: 0;">+<span id="LC1074" 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;">"[bus] --paired ignored; single/paired-end is inferred from number of files supplied"</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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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1076" 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">
1076
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<pre style="margin: 0;">+<span id="LC1076" 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;">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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1077" 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">
1077
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<pre style="margin: 0;">+<span id="LC1077" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" cannot specify batch mode and supply read files"</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="new_line diff-line-num new" data-linenumber="1078" 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">
1078
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<pre style="margin: 0;">+<span id="LC1078" 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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<td class="new_line diff-line-num new" data-linenumber="1079" 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">
1079
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<pre style="margin: 0;">+<span id="LC1079" 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="new_line diff-line-num new" data-linenumber="1080" 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">
1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check for batch files</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1081" 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">
1081
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<pre style="margin: 0;">+<span id="LC1081" 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="new_line diff-line-num new" data-linenumber="1082" 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">
1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1083" 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">
1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_file_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1084" 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">
1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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="new_line diff-line-num new" data-linenumber="1085" 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">
1085
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<pre style="margin: 0;">+<span id="LC1085" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</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;">batch_file_name</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="new_line diff-line-num new" data-linenumber="1086" 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">
1086
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<pre style="margin: 0;">+<span id="LC1086" 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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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="cpp"> <span class="p">}</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// open the file, parse and fill the batch_files values</span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" 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;">ifstream</span> <span class="n" style="color: #333;">bfile</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_file_name</span><span class="p">);</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" 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="n" style="color: #333;">line</span><span class="p">;</span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" 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="n" style="color: #333;">id</span><span class="p">,</span><span class="n" style="color: #333;">f1</span><span class="p">,</span><span class="n" style="color: #333;">f2</span><span class="p">;</span></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">read_first_batch_file_line</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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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</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;">getline</span><span class="p">(</span><span class="n" style="color: #333;">bfile</span><span class="p">,</span><span class="n" style="color: #333;">line</span><span class="p">))</span> <span class="p">{</span></span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</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;">0</span><span class="p">)</span> <span class="p">{</span></span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="cpp"> <span class="p">}</span></span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" 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;">stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" 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;">id</span><span class="p">;</span></span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'#'</span><span class="p">)</span> <span class="p">{</span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"> <span class="p">}</span></span>
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1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_ids</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">);</span></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" 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;">f1</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">f2</span><span class="p">;</span></span>
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1104
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<pre style="margin: 0;">+<span id="LC1104" 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;">read_first_batch_file_line</span><span class="p">)</span> <span class="p">{</span></span>
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1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f2</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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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">single_end</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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1107
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<pre style="margin: 0;">+<span id="LC1107" 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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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">single_end</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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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="cpp"> <span class="p">}</span></span>
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1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="cpp"> <span class="n" style="color: #333;">read_first_batch_file_line</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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1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="cpp"> <span class="p">}</span></span>
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1112
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<pre style="margin: 0;">+<span id="LC1112" 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;">single_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1113" 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">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">f1</span><span class="p">});</span></span>
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1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="cpp"> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1115" 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">
1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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="new_line diff-line-num new" data-linenumber="1116" 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">
1116
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<pre style="margin: 0;">+<span id="LC1116" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">f1</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="new_line diff-line-num new" data-linenumber="1117" 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">
1117
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<pre style="margin: 0;">+<span id="LC1117" 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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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="cpp"> <span class="p">}</span></span>
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1119
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<pre style="margin: 0;">+<span id="LC1119" 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;">f2</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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1120
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<pre style="margin: 0;">+<span id="LC1120" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" batch file malformatted"</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="new_line diff-line-num new" data-linenumber="1121" 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">
1121
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<pre style="margin: 0;">+<span id="LC1121" 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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1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1124" 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">
1124
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<pre style="margin: 0;">+<span id="LC1124" 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="new_line diff-line-num new" data-linenumber="1125" 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">
1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">f1</span><span class="p">,</span><span class="n" style="color: #333;">f2</span><span class="p">});</span></span>
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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="cpp"> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1127" 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">
1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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="new_line diff-line-num new" data-linenumber="1128" 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">
1128
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<pre style="margin: 0;">+<span id="LC1128" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">f1</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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1129
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<pre style="margin: 0;">+<span id="LC1129" 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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<td class="new_line diff-line-num new" data-linenumber="1130" 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">
1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1131" 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">
1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f2</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="new_line diff-line-num new" data-linenumber="1132" 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">
1132
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<pre style="margin: 0;">+<span id="LC1132" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" batch file malformatted"</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="new_line diff-line-num new" data-linenumber="1133" 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">
1133
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<pre style="margin: 0;">+<span id="LC1133" 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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<td class="new_line diff-line-num new" data-linenumber="1134" 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">
1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1135" 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">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1136" 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">
1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="cpp"> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1137" 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">
1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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="new_line diff-line-num new" data-linenumber="1138" 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">
1138
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<pre style="margin: 0;">+<span id="LC1138" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">f2</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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1139
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<pre style="margin: 0;">+<span id="LC1139" 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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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="cpp"> <span class="p">}</span></span>
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1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="cpp"> <span class="p">}</span></span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="cpp"> <span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="cpp"> <span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="cpp"> <span class="p">}</span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"> <span class="p">}</span></span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="cpp"> <span class="p">}</span></span>
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1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1148" 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">
1148
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<pre style="margin: 0;">+<span id="LC1148" 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;">pseudobam</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1149" 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">
1149
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<pre style="margin: 0;">+<span id="LC1149" 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: Pseudobam not supported yet in this mode"</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="new_line diff-line-num new" data-linenumber="1150" 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">
1150
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<pre style="margin: 0;">+<span id="LC1150" 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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1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="cpp"> <span class="p">}</span></span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" 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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1153
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<pre style="margin: 0;">+<span id="LC1153" 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: --bam not supported in this mode"</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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1154
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<pre style="margin: 0;">+<span id="LC1154" 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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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1156" 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">
1156
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<pre style="margin: 0;">+<span id="LC1156" 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;">tagsequence</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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1157
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<pre style="margin: 0;">+<span id="LC1157" 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: --tag not supported in this mode"</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="new_line diff-line-num new" data-linenumber="1158" 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">
1158
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<pre style="margin: 0;">+<span id="LC1158" 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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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="cpp"> <span class="p">}</span></span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" 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;">strand_specific</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;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">None</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1161" 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">
1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</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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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="cpp"> <span class="p">}</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" 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="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Set up BUS options</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1164" 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">
1164
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<pre style="margin: 0;">+<span id="LC1164" 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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1165
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<pre style="margin: 0;">+<span id="LC1165" 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="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;">0</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1166" 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">
1166
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<pre style="margin: 0;">+<span id="LC1166" 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="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1167" 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">
1167
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<pre style="margin: 0;">+<span id="LC1167" 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;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1168" 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">
1168
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<pre style="margin: 0;">+<span id="LC1168" 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;">single_end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1169" 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">
1169
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<pre style="margin: 0;">+<span id="LC1169" 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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<td class="new_line diff-line-num new" data-linenumber="1170" 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">
1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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1171
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<pre style="margin: 0;">+<span id="LC1171" 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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1172
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<pre style="margin: 0;">+<span id="LC1172" 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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1173
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<pre style="margin: 0;">+<span id="LC1173" 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="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;">0</span><span class="p">));</span></span>
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1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="cpp"> <span class="p">}</span></span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" 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="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="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;">1</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>
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1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="cpp"> <span class="p">}</span></span>
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1178
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<pre style="margin: 0;">+<span id="LC1178" 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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860
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1179
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<pre style="margin: 0;"> <span id="LC1179" 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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861
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1180
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<pre style="margin: 0;"> <span id="LC1180" 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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862
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1181
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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="cpp"> </span>
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863
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1182
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<pre style="margin: 0;"> <span id="LC1182" 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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864
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1183
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<pre style="margin: 0;"> <span id="LC1183" 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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1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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865
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1185
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<pre style="margin: 0;"> <span id="LC1185" 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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866
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1186
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<pre style="margin: 0;"> <span id="LC1186" 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="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;">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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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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1187
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<pre style="margin: 0;">+<span id="LC1187" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span> <span class="c1" style="color: #998; font-style: italic;">// first file [16:26]</span></span>
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868
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1188
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<pre style="margin: 0;"> <span id="LC1188" 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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869
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1189
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<pre style="margin: 0;"> <span id="LC1189" 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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870
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1190
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<pre style="margin: 0;"> <span id="LC1190" 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="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;">0</span><span class="p">));</span></span>
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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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1191
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<pre style="margin: 0;">+<span id="LC1191" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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872
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1192
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<pre style="margin: 0;"> <span id="LC1192" 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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873
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1193
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<pre style="margin: 0;"> <span id="LC1193" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// } else if (opt.technology == "10XV1") {</span></span>
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874
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1194
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<pre style="margin: 0;"> <span id="LC1194" class="line" lang="cpp"></span>
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875
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1195
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<pre style="margin: 0;"> <span id="LC1195" 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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1196
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<pre style="margin: 0;"> <span id="LC1196" 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="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;">0</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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1197
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<pre style="margin: 0;">+<span id="LC1197" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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1198
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<pre style="margin: 0;"> <span id="LC1198" 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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1199
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<pre style="margin: 0;"> <span id="LC1199" 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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1200
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<pre style="margin: 0;"> <span id="LC1200" 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="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;">0</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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1201
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<pre style="margin: 0;">+<span id="LC1201" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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882
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1202
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<pre style="margin: 0;"> <span id="LC1202" 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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883
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1203
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<pre style="margin: 0;"> <span id="LC1203" 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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884
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1204
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<pre style="margin: 0;"> <span id="LC1204" 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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1205
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<pre style="margin: 0;"> <span id="LC1205" 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="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;">0</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC886" 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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1206
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<pre style="margin: 0;">+<span id="LC1206" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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887
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1207
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<pre style="margin: 0;"> <span id="LC1207" 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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1208
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<pre style="margin: 0;"> <span id="LC1208" 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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889
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1209
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<pre style="margin: 0;"> <span id="LC1209" 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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890
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1210
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<pre style="margin: 0;"> <span id="LC1210" 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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891
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1211
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<pre style="margin: 0;"> <span id="LC1211" 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="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;">0</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="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1212
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<pre style="margin: 0;">+<span id="LC1212" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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893
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1213
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<pre style="margin: 0;"> <span id="LC1213" 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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894
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1214
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<pre style="margin: 0;"> <span id="LC1214" 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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895
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1215
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<pre style="margin: 0;"> <span id="LC1215" 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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896
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1216
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<pre style="margin: 0;"> <span id="LC1216" 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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897
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1217
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<pre style="margin: 0;"> <span id="LC1217" 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="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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898
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<pre style="margin: 0;">-<span id="LC898" 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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1218
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<pre style="margin: 0;">+<span id="LC1218" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC1219" 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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900
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1220
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<pre style="margin: 0;"> <span id="LC1220" 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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901
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1221
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<pre style="margin: 0;"> <span id="LC1221" 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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902
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1222
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<pre style="margin: 0;"> <span id="LC1222" 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="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;">0</span><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="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1223
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<pre style="margin: 0;">+<span id="LC1223" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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904
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1224
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<pre style="margin: 0;"> <span id="LC1224" 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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905
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1225
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<pre style="margin: 0;"> <span id="LC1225" 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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906
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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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</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;">0</span><span class="p">));</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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1227
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<pre style="margin: 0;">+<span id="LC1227" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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908
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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;">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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1229
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<pre style="margin: 0;">+<span id="LC1229" 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;">"SPLIT-SEQ"</span><span class="p">)</span> <span class="p">{</span></span>
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1230
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<pre style="margin: 0;">+<span id="LC1230" 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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1231
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<pre style="margin: 0;">+<span id="LC1231" 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="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;">0</span><span class="p">));</span></span>
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1232
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<pre style="margin: 0;">+<span id="LC1232" 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="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;">10</span><span class="p">));</span></span>
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1233
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<pre style="margin: 0;">+<span id="LC1233" 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;">10</span><span class="p">,</span><span class="mi" style="color: #099;">18</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC1234" 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;">48</span><span class="p">,</span><span class="mi" style="color: #099;">56</span><span class="p">));</span></span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" 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;">78</span><span class="p">,</span><span class="mi" style="color: #099;">86</span><span class="p">));</span></span>
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909
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1236
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<pre style="margin: 0;"> <span id="LC1236" 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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910
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1237
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<pre style="margin: 0;"> <span id="LC1237" 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="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;">0</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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1238
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<pre style="margin: 0;">+<span id="LC1238" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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912
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1239
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<pre style="margin: 0;"> <span id="LC1239" 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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913
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1240
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<pre style="margin: 0;"> <span id="LC1240" 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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914
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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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</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;">0</span><span class="p">));</span></span>
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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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1242
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<pre style="margin: 0;">+<span id="LC1242" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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916
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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;">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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1244
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<pre style="margin: 0;">+<span id="LC1244" 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;">"SMARTSEQ3"</span><span class="p">)</span> <span class="p">{</span></span>
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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;">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;">4</span><span class="p">;</span></span>
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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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</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;">22</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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1247
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<pre style="margin: 0;">+<span id="LC1247" 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="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;">3</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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1248
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<pre style="margin: 0;">+<span id="LC1248" 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="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;">19</span><span class="p">));</span></span>
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1249
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<pre style="margin: 0;">+<span id="LC1249" 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;">0</span><span class="p">));</span></span>
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1250
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<pre style="margin: 0;">+<span id="LC1250" 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;">0</span><span class="p">));</span></span>
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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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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1252
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<pre style="margin: 0;">+<span id="LC1252" 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;">"BULK"</span><span class="p">)</span> <span class="p">{</span></span>
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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;">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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1254
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<pre style="margin: 0;">+<span id="LC1254" 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="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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1255
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<pre style="margin: 0;">+<span id="LC1255" 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="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="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;">1</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>
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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;">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;">0</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;">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;">0</span><span class="p">));</span></span>
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1258
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<pre style="margin: 0;">+<span id="LC1258" 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;">single_end</span><span class="p">)</span> <span class="p">{</span></span>
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1259
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<pre style="margin: 0;">+<span id="LC1259" 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="p">;</span></span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" 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="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;">3</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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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="cpp"> <span class="p">}</span></span>
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1263
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<pre style="margin: 0;">+<span id="LC1263" 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;">"BDWTA"</span><span class="p">)</span> <span class="p">{</span></span>
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1264
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<pre style="margin: 0;">+<span id="LC1264" 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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1265
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<pre style="margin: 0;">+<span id="LC1265" 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;">9</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// bc1 CLS1</span></span>
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1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// busopt.bc.push_back(BUSOptionSubstr(0,9,9+12)); // linker</span></span>
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1267
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<pre style="margin: 0;">+<span id="LC1267" 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;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// bc2 CLS2</span></span>
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1268
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// busopt.bc.push_back(BUSOptionSubstr(0,9+12+9,9+12+9+13)); // linker</span></span>
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1269
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<pre style="margin: 0;">+<span id="LC1269" 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;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">13</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">13</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// bc3 CLS3</span></span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" 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="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;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">13</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">13</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">8</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// umi</span></span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" 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="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;">0</span><span class="p">));</span></span>
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1272
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<pre style="margin: 0;"> <span id="LC1272" 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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918
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1273
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<pre style="margin: 0;"> <span id="LC1273" 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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919
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1274
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<pre style="margin: 0;"> <span id="LC1274" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="922" style="width: 35px; color: rgba(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">@@ -922,13 +1277,17 @@ bool CheckOptionsBus(ProgramOptions& opt) {</td>
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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;">//bool invalid = ParseTechnology(opt.technology, values, files, errorList, bcValues);</span></span>
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">valid</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;">busopt</span><span class="p">,</span> <span class="n" style="color: #333;">errorList</span><span class="p">);</span></span>
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924
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> </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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</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="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="p">{</span></span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="cpp"> <span class="p">}</span></span>
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1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp"> </span>
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925
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1284
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<pre style="margin: 0;"> <span id="LC1284" 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;">valid</span><span class="p">)</span> <span class="p">{</span></span>
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926
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1285
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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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927
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1286
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<pre style="margin: 0;"> <span id="LC1286" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> busopt.nfiles = files.size(); </span></span>
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1287
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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for(int i = 0; i < bcValues.size(); i++) {</span></span>
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1288
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<pre style="margin: 0;"> <span id="LC1288" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> busopt.bc.push_back(bcValues[i]);</span></span>
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930
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1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> busopt.umi<span class="idiff left right"> = </span>values[0];</span></span>
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1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> busopt.umi<span class="idiff left">.push_back(</span>values[0]<span class="idiff right">)</span>;</span></span>
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1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> busopt.seq.push_back(values[1]);</span></span>
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1292
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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1293
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<pre style="margin: 0;"> <span id="LC1293" 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 unfold js-unfold old_line" data-linenumber="940" style="width: 35px; color: rgba(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="1299" style="width: 35px; color: rgba(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">@@ -940,72 +1299,116 @@ bool CheckOptionsBus(ProgramOptions& opt) {</td>
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940
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1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="cpp"> <span class="p">}</span></span>
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941
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1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="cpp"> <span class="p">}</span></span>
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942
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1301
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<pre style="margin: 0;"> <span id="LC1301" 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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1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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943
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1303
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<pre style="margin: 0;"> <span id="LC1303" 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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944
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1304
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<pre style="margin: 0;"> <span id="LC1304" 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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945
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1305
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<pre style="margin: 0;"> <span id="LC1305" 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="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;">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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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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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="new_line diff-line-num new" data-linenumber="1306" 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">
1306
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<pre style="margin: 0;">+<span id="LC1306" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span> <span class="c1" style="color: #998; font-style: italic;">// first file [16:26]</span></span>
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947
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1307
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<pre style="margin: 0;"> <span id="LC1307" 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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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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948
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1309
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<pre style="margin: 0;"> <span id="LC1309" 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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949
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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;">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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950
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1311
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<pre style="margin: 0;"> <span id="LC1311" 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="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;">0</span><span class="p">));</span></span>
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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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1312
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<pre style="margin: 0;">+<span id="LC1312" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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952
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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;">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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1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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1315
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<pre style="margin: 0;">+<span id="LC1315" 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;">"VISIUM"</span><span class="p">)</span> <span class="p">{</span></span>
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1316
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<pre style="margin: 0;">+<span id="LC1316" 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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1317
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<pre style="margin: 0;">+<span id="LC1317" 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="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;">0</span><span class="p">));</span></span>
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1318
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<pre style="margin: 0;">+<span id="LC1318" 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="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;">16</span><span class="p">,</span><span class="mi" style="color: #099;">28</span><span class="p">));</span></span>
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1319
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<pre style="margin: 0;">+<span id="LC1319" 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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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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953
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1321
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<pre style="margin: 0;"> <span id="LC1321" 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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954
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1322
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<pre style="margin: 0;"> <span id="LC1322" 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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955
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1323
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<pre style="margin: 0;"> <span id="LC1323" 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="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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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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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;">10</span><span class="p">);</span></span>
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1324
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<pre style="margin: 0;">+<span id="LC1324" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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;">10</span><span class="p">)<span class="idiff right">)</span>;</span></span>
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957
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1325
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<pre style="margin: 0;"> <span id="LC1325" 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;">14</span><span class="p">));</span></span>
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1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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958
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1327
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<pre style="margin: 0;"> <span id="LC1327" 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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959
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1328
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<pre style="margin: 0;"> <span id="LC1328" 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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960
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1329
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<pre style="margin: 0;"> <span id="LC1329" 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="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;">0</span><span class="p">));</span></span>
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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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1330
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<pre style="margin: 0;">+<span id="LC1330" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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962
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1331
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<pre style="margin: 0;"> <span id="LC1331" 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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963
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1332
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<pre style="margin: 0;"> <span id="LC1332" 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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964
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1333
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<pre style="margin: 0;"> <span id="LC1333" 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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1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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965
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1335
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<pre style="margin: 0;"> <span id="LC1335" 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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966
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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;">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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967
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1337
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<pre style="margin: 0;"> <span id="LC1337" 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="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;">0</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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1338
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<pre style="margin: 0;">+<span id="LC1338" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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969
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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;">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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970
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1340
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<pre style="margin: 0;"> <span id="LC1340" 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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971
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1341
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<pre style="margin: 0;"> <span id="LC1341" 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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1342
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<pre style="margin: 0;"> <span id="LC1342" 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="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;">0</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC973" 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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1343
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<pre style="margin: 0;">+<span id="LC1343" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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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;">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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<pre style="margin: 0;">-<span id="LC975" 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 class="idiff left right"> </span></span>
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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;">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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976
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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 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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1347
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<pre style="margin: 0;"> <span id="LC1347" 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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1348
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<pre style="margin: 0;"> <span id="LC1348" 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="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;">0</span><span class="p">));</span></span>
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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;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1349
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<pre style="margin: 0;">+<span id="LC1349" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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1350
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<pre style="margin: 0;"> <span id="LC1350" 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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<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;">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 class="idiff left right"> </span></span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" 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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1352
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<pre style="margin: 0;"> <span id="LC1352" 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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1353
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<pre style="margin: 0;"> <span id="LC1353" 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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<pre style="margin: 0;"> <span id="LC1354" 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="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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<pre style="margin: 0;">-<span id="LC985" 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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1355
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<pre style="margin: 0;">+<span id="LC1355" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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1356
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<pre style="margin: 0;"> <span id="LC1356" 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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1357
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<pre style="margin: 0;"> <span id="LC1357" 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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1358
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<pre style="margin: 0;"> <span id="LC1358" 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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989
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1359
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<pre style="margin: 0;"> <span id="LC1359" 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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1360
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<pre style="margin: 0;"> <span id="LC1360" 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="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;">0</span><span class="p">));</span></span>
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991
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<pre style="margin: 0;">-<span id="LC991" 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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1361
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<pre style="margin: 0;">+<span id="LC1361" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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992
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1362
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<pre style="margin: 0;"> <span id="LC1362" 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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1363
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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1364
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<pre style="margin: 0;"> <span id="LC1364" 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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1365
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<pre style="margin: 0;"> <span id="LC1365" 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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995
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1366
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<pre style="margin: 0;"> <span id="LC1366" 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="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;">0</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC996" 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="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1367
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<pre style="margin: 0;">+<span id="LC1367" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC1368" 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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1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" 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;">"SPLIT-SEQ"</span><span class="p">){</span></span>
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1371
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<pre style="margin: 0;">+<span id="LC1371" 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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1372
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<pre style="margin: 0;">+<span id="LC1372" 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="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;">0</span><span class="p">));</span></span>
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1373
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<pre style="margin: 0;">+<span id="LC1373" 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="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;">10</span><span class="p">));</span></span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" 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;">10</span><span class="p">,</span><span class="mi" style="color: #099;">18</span><span class="p">));</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" 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;">48</span><span class="p">,</span><span class="mi" style="color: #099;">56</span><span class="p">));</span></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" 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;">78</span><span class="p">,</span><span class="mi" style="color: #099;">86</span><span class="p">));</span></span>
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998
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1377
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<pre style="margin: 0;"> <span id="LC1377" 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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1378
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<pre style="margin: 0;"> <span id="LC1378" 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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1000
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1379
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<pre style="margin: 0;"> <span id="LC1379" 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="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;">0</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;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </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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1380
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<pre style="margin: 0;">+<span id="LC1380" 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="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">push_back</span></span><span class="p"><span class="idiff">(</span></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 class="idiff right">)</span>;</span></span>
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1002
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1381
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<pre style="margin: 0;"> <span id="LC1381" 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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1003
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<pre style="margin: 0;">-<span id="LC1003" 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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1382
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<pre style="margin: 0;">+<span id="LC1382" 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;">"SMARTSEQ3"</span><span class="p">)</span> <span class="p">{</span></span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" 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;">4</span><span class="p">;</span></span>
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1384
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<pre style="margin: 0;">+<span id="LC1384" 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="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;">22</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" 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="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;">3</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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1386
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<pre style="margin: 0;">+<span id="LC1386" 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="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;">19</span><span class="p">));</span></span>
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1387
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<pre style="margin: 0;">+<span id="LC1387" 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;">0</span><span class="p">));</span></span>
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1388
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<pre style="margin: 0;">+<span id="LC1388" 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;">0</span><span class="p">));</span></span>
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1389
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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1390
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<pre style="margin: 0;">+<span id="LC1390" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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1391
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<pre style="margin: 0;">+<span id="LC1391" 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;">"BULK"</span><span class="p">)</span> <span class="p">{</span></span>
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1004
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1392
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<pre style="margin: 0;"> <span id="LC1392" 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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1005
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1393
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<pre style="margin: 0;"> <span id="LC1393" 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="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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1006
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<pre style="margin: 0;">-<span id="LC1006" 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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1007
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<pre style="margin: 0;">-<span id="LC1007" 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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1008
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<pre style="margin: 0;">-<span id="LC1008" 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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1394
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<pre style="margin: 0;">+<span id="LC1394" 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="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="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;">1</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>
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1395
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<pre style="margin: 0;">+<span id="LC1395" 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;">0</span><span class="p">));</span></span>
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1396
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<pre style="margin: 0;">+<span id="LC1396" 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;">0</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1397" 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">
1397
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<pre style="margin: 0;">+<span id="LC1397" 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;">single_end</span><span class="p">)</span> <span class="p">{</span></span>
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1398
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<pre style="margin: 0;">+<span id="LC1398" 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="p">;</span></span>
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1399
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<pre style="margin: 0;">+<span id="LC1399" 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="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;">3</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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1400
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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1401
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<pre style="margin: 0;">+<span id="LC1401" class="line" lang="cpp"> <span class="p">}</span></span>
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1402
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<pre style="margin: 0;">+<span id="LC1402" 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;">"BDWTA"</span><span class="p">)</span> <span class="p">{</span></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" 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="new_line diff-line-num new" data-linenumber="1404" 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">
1404
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<pre style="margin: 0;">+<span id="LC1404" 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;">9</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// bc1 CLS1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1405" 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">
1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// busopt.bc.push_back(BUSOptionSubstr(0,9,9+12)); // linker</span></span>
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1406
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<pre style="margin: 0;">+<span id="LC1406" 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;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// bc2 CLS2</span></span>
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1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// busopt.bc.push_back(BUSOptionSubstr(0,9+12+9,9+12+9+13)); // linker</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" 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;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">13</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">13</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// bc3 CLS3</span></span>
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1409
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<pre style="margin: 0;">+<span id="LC1409" 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="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;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">13</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">13</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">9</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">8</span><span class="p">));</span> <span class="c1" style="color: #998; font-style: italic;">// umi</span></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" 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="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;">0</span><span class="p">));</span></span>
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1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="cpp"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">;</span></span>
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1009
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1412
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<pre style="margin: 0;"> <span id="LC1412" 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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1010
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1413
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<pre style="margin: 0;"> <span id="LC1413" 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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1011
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1414
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<pre style="margin: 0;"> <span id="LC1414" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1014" style="width: 35px; color: rgba(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="1417" style="width: 35px; color: rgba(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">@@ -1014,6 +1417,9 @@ bool CheckOptionsBus(ProgramOptions& opt) {</td>
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1014
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1417
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<pre style="margin: 0;"> <span id="LC1417" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//bool invalid = ParseTechnology(opt.technology, values, files, errorList, bcValues);</span></span>
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1015
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1418
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">valid</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;">busopt</span><span class="p">,</span> <span class="n" style="color: #333;">errorList</span><span class="p">);</span></span>
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1016
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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="old_line diff-line-num new" data-linenumber="1017" 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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1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">seq</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="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="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1421" 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">
1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="cpp"> <span class="p">}</span></span>
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1017
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1423
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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="cpp"> </span>
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1018
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1424
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<pre style="margin: 0;"> <span id="LC1424" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">)</span> <span class="p">{</span></span>
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1019
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1425
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<pre style="margin: 0;"> <span id="LC1425" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1021" style="width: 35px; color: rgba(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="1427" style="width: 35px; color: rgba(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">@@ -1021,7 +1427,7 @@ bool CheckOptionsBus(ProgramOptions& opt) {</td>
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1021
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1427
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<pre style="margin: 0;"> <span id="LC1427" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for(int i = 0; i < bcValues.size(); i++) {</span></span>
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1022
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1428
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<pre style="margin: 0;"> <span id="LC1428" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> busopt.bc.push_back(bcValues[i]);</span></span>
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1023
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1429
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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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1024
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<pre style="margin: 0;">-<span id="LC1024" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> busopt.umi<span class="idiff left right"> = </span>values[0];</span></span>
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1430
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<pre style="margin: 0;">+<span id="LC1430" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> busopt.umi<span class="idiff left">.push_back(</span>values[0]<span class="idiff right">)</span>;</span></span>
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1025
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1431
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<pre style="margin: 0;"> <span id="LC1431" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> busopt.seq.push_back(values[1]);</span></span>
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1026
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1432
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<pre style="margin: 0;"> <span id="LC1432" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1027
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1433
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<pre style="margin: 0;"> <span id="LC1433" 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 unfold js-unfold old_line" data-linenumber="1034" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1034,10 +1440,50 @@ bool CheckOptionsBus(ProgramOptions& opt) {</td>
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1034
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1440
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<pre style="margin: 0;"> <span id="LC1440" class="line" lang="cpp"> <span class="p">}</span></span>
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1035
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1441
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<pre style="margin: 0;"> <span id="LC1441" class="line" lang="cpp"> <span class="p">}</span></span>
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1036
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1442
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="cpp"> <span class="p">}</span></span>
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1443
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="cpp"> </span>
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1444
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<pre style="margin: 0;">+<span id="LC1444" 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;">tagsequence</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</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;">"SMARTSEQ3"</span><span class="p">))</span> <span class="p">{</span></span>
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1445
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<pre style="margin: 0;">+<span id="LC1445" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">tagsequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ATTGCGCAATG"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1446" 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">
1446
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<pre style="margin: 0;">+<span id="LC1446" 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;">"[bus] Using "</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;">tagsequence</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" as UMI tag sequence"</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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1447
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<pre style="margin: 0;">+<span id="LC1447" class="line" lang="cpp"> <span class="p">}</span></span>
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1448
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<pre style="margin: 0;">+<span id="LC1448" class="line" lang="cpp"> </span>
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1449
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<pre style="margin: 0;">+<span id="LC1449" 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;">strand_specific</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;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">None</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1450" 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">
1450
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<pre style="margin: 0;">+<span id="LC1450" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</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;">// User specified --unstranded</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1451" 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">
1451
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<pre style="margin: 0;">+<span id="LC1451" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ret</span><span class="p">)</span> <span class="p">{</span></span>
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1452
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strand</span><span class="p">;</span></span>
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1453
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<pre style="margin: 0;">+<span id="LC1453" 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;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FR</span><span class="p">)</span> <span class="p">{</span></span>
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1454
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<pre style="margin: 0;">+<span id="LC1454" 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;">"[bus] Note: Strand option was not specified; setting it to --fr-stranded for specified 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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1455
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<pre style="margin: 0;">+<span id="LC1455" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</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="new_line diff-line-num new" data-linenumber="1456" 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">
1456
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<pre style="margin: 0;">+<span id="LC1456" 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;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ProgramOptions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrandType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RF</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1457" 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">
1457
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<pre style="margin: 0;">+<span id="LC1457" 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;">"[bus] Note: Strand option was not specified; setting it to --rf-stranded for specified 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="new_line diff-line-num new" data-linenumber="1458" 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">
1458
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<pre style="margin: 0;">+<span id="LC1458" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">strand_specific</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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1459
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<pre style="margin: 0;">+<span id="LC1459" 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="new_line diff-line-num new" data-linenumber="1460" 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">
1460
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<pre style="margin: 0;">+<span id="LC1460" 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;">"[bus] Note: Strand option was not specified; setting it to --unstranded for specified 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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1461
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<pre style="margin: 0;">+<span id="LC1461" class="line" lang="cpp"> <span class="p">}</span></span>
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1462
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<pre style="margin: 0;">+<span id="LC1462" class="line" lang="cpp"> <span class="p">}</span></span>
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1463
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="cpp"> </span>
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1464
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<pre style="margin: 0;">+<span id="LC1464" 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;">tagsequence</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="new_line diff-line-num new" data-linenumber="1465" 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">
1465
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<pre style="margin: 0;">+<span id="LC1465" class="line" lang="cpp"> <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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">start</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;">tagsequence</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1466" 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">
1466
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<pre style="margin: 0;">+<span id="LC1466" 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;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">start</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;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">stop</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1467" 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">
1467
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<pre style="margin: 0;">+<span id="LC1467" 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: Tag sequence must be shorter than UMI sequence"</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="new_line diff-line-num new" data-linenumber="1468" 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">
1468
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<pre style="margin: 0;">+<span id="LC1468" 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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<td class="new_line diff-line-num new" data-linenumber="1469" 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">
1469
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<pre style="margin: 0;">+<span id="LC1469" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1470" 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">
1470
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<pre style="margin: 0;">+<span id="LC1470" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1471" 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">
1471
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<pre style="margin: 0;">+<span id="LC1471" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1472" 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">
1472
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<pre style="margin: 0;">+<span id="LC1472" 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;">single_end</span> <span class="o" style="font-weight: 600;">&&</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;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1473" 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">
1473
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<pre style="margin: 0;">+<span id="LC1473" 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: Paired reads are not compatible with the specified 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="new_line diff-line-num new" data-linenumber="1474" 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">
1474
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<pre style="margin: 0;">+<span id="LC1474" 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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1475
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<pre style="margin: 0;">+<span id="LC1475" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1476" 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">
1476
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<pre style="margin: 0;">+<span id="LC1476" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="1477" 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">
1477
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<pre style="margin: 0;">+<span id="LC1477" 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;">strand_specific</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" 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">
1478
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<pre style="margin: 0;">+<span id="LC1478" 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;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">seq</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;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</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 class="n" style="color: #333;">seq</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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">paired</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1479" 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">
1479
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<pre style="margin: 0;">+<span id="LC1479" 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: Strand-specific read processing is only supported for technologies with a single CDNA read file or paired-end reads"</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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1480
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<pre style="margin: 0;">+<span id="LC1480" 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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1481
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<pre style="margin: 0;">+<span id="LC1481" class="line" lang="cpp"> <span class="p">}</span></span>
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1482
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<pre style="margin: 0;">+<span id="LC1482" class="line" lang="cpp"> <span class="p">}</span></span>
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1037
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1483
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<pre style="margin: 0;"> <span id="LC1483" class="line" lang="cpp"></span>
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1038
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1484
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<pre style="margin: 0;"> <span id="LC1484" 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;">genomebam</span><span class="p">)</span> <span class="p">{</span></span>
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1039
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<pre style="margin: 0;">-<span id="LC1039" 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;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">seq</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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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1040
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<pre style="margin: 0;">-<span id="LC1040" 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: BAM output is currently only supported for technologies with a single CDNA read file"</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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1485
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<pre style="margin: 0;">+<span id="LC1485" 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;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">seq</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;">1</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="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">busOptions</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</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="mi" style="color: #099;"><span class="idiff">2</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">opt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">busOptions</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">paired</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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1486
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<pre style="margin: 0;">+<span id="LC1486" 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: BAM output is currently only supported for technologies with a single CDNA read file<span class="idiff left right"> or paired-end reads</span>"</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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1041
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1487
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<pre style="margin: 0;"> <span id="LC1487" 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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1488
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<pre style="margin: 0;"> <span id="LC1488" class="line" lang="cpp"> <span class="p">}</span></span>
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1043
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1489
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<pre style="margin: 0;"> <span id="LC1489" 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;">gtfFile</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 unfold js-unfold old_line" data-linenumber="1285" style="width: 35px; color: rgba(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="1731" style="width: 35px; color: rgba(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">@@ -1285,24 +1731,179 @@ bool CheckOptionsEM(ProgramOptions& opt, bool emonly = false) {</td>
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1731
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<pre style="margin: 0;"> <span id="LC1731" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//ret = false;</span></span>
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1732
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<pre style="margin: 0;"> <span id="LC1732" class="line" lang="cpp"> <span class="p">}</span></span>
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1733
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<pre style="margin: 0;"> <span id="LC1733" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1288" class="line" lang="cpp"></span>
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1734
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<pre style="margin: 0;">+<span id="LC1734" class="line" lang="cpp"></span>
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1735
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<pre style="margin: 0;">+<span id="LC1735" 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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1736
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<pre style="margin: 0;">+<span id="LC1736" 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 bootstrap samples must be a non-negative integer."</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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1737
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<pre style="margin: 0;">+<span id="LC1737" 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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1738
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<pre style="margin: 0;">+<span id="LC1738" class="line" lang="cpp"> <span class="p">}</span></span>
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1739
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<pre style="margin: 0;">+<span id="LC1739" class="line" lang="cpp"></span>
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1740
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<pre style="margin: 0;">+<span id="LC1740" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifndef USE_HDF5 </span></span>
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1741
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<pre style="margin: 0;">+<span id="LC1741" 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="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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1742
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<pre style="margin: 0;">+<span id="LC1742" 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: kallisto was not compiled with HDF5 support so no bootstrapping"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1743" 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">
1743
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<pre style="margin: 0;">+<span id="LC1743" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"will be performed. Run quant with --plaintext option or recompile with"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1744
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<pre style="margin: 0;">+<span id="LC1744" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"HDF5 support to obtain bootstrap estimates."</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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1745
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<pre style="margin: 0;">+<span id="LC1745" class="line" lang="cpp"> <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>
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1746
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<pre style="margin: 0;">+<span id="LC1746" class="line" lang="cpp"> <span class="p">}</span></span>
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1747
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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1748
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<pre style="margin: 0;">+<span id="LC1748" 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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1749
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<pre style="margin: 0;">+<span id="LC1749" class="line" lang="cpp"><span class="p">}</span></span>
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1750
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<pre style="margin: 0;">+<span id="LC1750" class="line" lang="cpp"></span>
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1751
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<pre style="margin: 0;">+<span id="LC1751" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">CheckOptionsTCCQuant</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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1752
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<pre style="margin: 0;">+<span id="LC1752" class="line" lang="cpp"> </span>
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1753
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<pre style="margin: 0;">+<span id="LC1753" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ret</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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1754
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<pre style="margin: 0;">+<span id="LC1754" class="line" lang="cpp"> </span>
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1755
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<pre style="margin: 0;">+<span id="LC1755" 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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1756
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<pre style="margin: 0;">+<span id="LC1756" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check for index</span></span>
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1757
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<pre style="margin: 0;">+<span id="LC1757" 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;">index</span><span class="p">.</span><span class="n" style="color: #333;">empty</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;">transcriptsFile</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="new_line diff-line-num new" data-linenumber="1758" 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">
1758
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<pre style="margin: 0;">+<span id="LC1758" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" either a kallisto index file or a transcripts file need to be supplied"</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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1759
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<pre style="margin: 0;">+<span id="LC1759" 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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<td class="new_line diff-line-num new" data-linenumber="1760" 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">
1760
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<pre style="margin: 0;">+<span id="LC1760" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</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;">transcriptsFile</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="new_line diff-line-num new" data-linenumber="1761" 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">
1761
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<pre style="margin: 0;">+<span id="LC1761" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" cannot supply both a kallisto index file and a transcripts file"</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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1762
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<pre style="margin: 0;">+<span id="LC1762" 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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1763
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<pre style="margin: 0;">+<span id="LC1763" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">index</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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1764
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<pre style="margin: 0;">+<span id="LC1764" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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1765
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<pre style="margin: 0;">+<span id="LC1765" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intStat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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1766
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<pre style="margin: 0;">+<span id="LC1766" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intStat</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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1767
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<pre style="margin: 0;">+<span id="LC1767" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" kallisto index file not found "</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;">index</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="new_line diff-line-num new" data-linenumber="1768" 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">
1768
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<pre style="margin: 0;">+<span id="LC1768" 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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1769
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<pre style="margin: 0;">+<span id="LC1769" class="line" lang="cpp"> <span class="p">}</span></span>
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1770
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<pre style="margin: 0;">+<span id="LC1770" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">transcriptsFile</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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1771
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<pre style="margin: 0;">+<span id="LC1771" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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1772
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<pre style="margin: 0;">+<span id="LC1772" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intStat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">transcriptsFile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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1773
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<pre style="margin: 0;">+<span id="LC1773" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intStat</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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1774
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<pre style="margin: 0;">+<span id="LC1774" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" transcripts file not found "</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;">transcriptsFile</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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1775
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<pre style="margin: 0;">+<span id="LC1775" 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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1776
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<pre style="margin: 0;">+<span id="LC1776" class="line" lang="cpp"> <span class="p">}</span></span>
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1777
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<pre style="margin: 0;">+<span id="LC1777" class="line" lang="cpp"> <span class="p">}</span></span>
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1778
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<pre style="margin: 0;">+<span id="LC1778" class="line" lang="cpp"></span>
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1779
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<pre style="margin: 0;">+<span id="LC1779" 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;">tccFile</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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1780
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<pre style="margin: 0;">+<span id="LC1780" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" transcript-compatibility counts file missing"</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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1781
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<pre style="margin: 0;">+<span id="LC1781" 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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1782
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<pre style="margin: 0;">+<span id="LC1782" 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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1783
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<pre style="margin: 0;">+<span id="LC1783" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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1784
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<pre style="margin: 0;">+<span id="LC1784" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intStat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">tccFile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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1785
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<pre style="margin: 0;">+<span id="LC1785" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intStat</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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1786
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<pre style="margin: 0;">+<span id="LC1786" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" transcript-compatibility counts file not found "</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;">tccFile</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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1787
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<pre style="margin: 0;">+<span id="LC1787" 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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1788
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<pre style="margin: 0;">+<span id="LC1788" class="line" lang="cpp"> <span class="p">}</span></span>
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1789
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<pre style="margin: 0;">+<span id="LC1789" class="line" lang="cpp"> <span class="p">}</span></span>
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1790
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<pre style="margin: 0;">+<span id="LC1790" class="line" lang="cpp"> </span>
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1791
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<pre style="margin: 0;">+<span id="LC1791" 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;">ecFile</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</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;">transcriptsFile</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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1792
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<pre style="margin: 0;">+<span id="LC1792" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" equivalence class file must be supplied if transcripts file is supplied "</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;">tccFile</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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1793
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<pre style="margin: 0;">+<span id="LC1793" 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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1794
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<pre style="margin: 0;">+<span id="LC1794" class="line" lang="cpp"> <span class="p">}</span></span>
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1795
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<pre style="margin: 0;">+<span id="LC1795" class="line" lang="cpp"></span>
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1796
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<pre style="margin: 0;">+<span id="LC1796" 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;">ecFile</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="new_line diff-line-num new" data-linenumber="1797" 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">
1797
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<pre style="margin: 0;">+<span id="LC1797" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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1798
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<pre style="margin: 0;">+<span id="LC1798" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intStat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">ecFile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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1799
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<pre style="margin: 0;">+<span id="LC1799" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intStat</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="new_line diff-line-num new" data-linenumber="1800" 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">
1800
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<pre style="margin: 0;">+<span id="LC1800" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" equivalence class file not found "</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;">ecFile</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="new_line diff-line-num new" data-linenumber="1801" 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">
1801
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<pre style="margin: 0;">+<span id="LC1801" 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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1802
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<pre style="margin: 0;">+<span id="LC1802" class="line" lang="cpp"> <span class="p">}</span></span>
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1803
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<pre style="margin: 0;">+<span id="LC1803" class="line" lang="cpp"> <span class="p">}</span></span>
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1804
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<pre style="margin: 0;">+<span id="LC1804" class="line" lang="cpp"> </span>
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1805
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<pre style="margin: 0;">+<span id="LC1805" 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;">fldFile</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="new_line diff-line-num new" data-linenumber="1806" 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">
1806
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<pre style="margin: 0;">+<span id="LC1806" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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1807
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<pre style="margin: 0;">+<span id="LC1807" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intStat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fldFile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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1808
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<pre style="margin: 0;">+<span id="LC1808" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intStat</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="new_line diff-line-num new" data-linenumber="1809" 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">
1809
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<pre style="margin: 0;">+<span id="LC1809" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" fragment length distribution file not found "</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;">fldFile</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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1810
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<pre style="margin: 0;">+<span id="LC1810" 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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1811
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<pre style="margin: 0;">+<span id="LC1811" class="line" lang="cpp"> <span class="p">}</span></span>
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1812
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<pre style="margin: 0;">+<span id="LC1812" class="line" lang="cpp"> <span class="p">}</span></span>
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1813
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<pre style="margin: 0;">+<span id="LC1813" class="line" lang="cpp"> </span>
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1814
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<pre style="margin: 0;">+<span id="LC1814" 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;">genemap</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</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;">gtfFile</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="new_line diff-line-num new" data-linenumber="1815" 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">
1815
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<pre style="margin: 0;">+<span id="LC1815" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Cannot supply both --genemap and --gtf"</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="new_line diff-line-num new" data-linenumber="1816" 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">
1816
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<pre style="margin: 0;">+<span id="LC1816" 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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1817
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<pre style="margin: 0;">+<span id="LC1817" class="line" lang="cpp"> <span class="p">}</span></span>
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1818
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<pre style="margin: 0;">+<span id="LC1818" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1819" 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">
1819
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<pre style="margin: 0;">+<span id="LC1819" 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;">gtfFile</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="new_line diff-line-num new" data-linenumber="1820" 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">
1820
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<pre style="margin: 0;">+<span id="LC1820" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1821" 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">
1821
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<pre style="margin: 0;">+<span id="LC1821" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intStat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">gtfFile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1822" 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">
1822
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<pre style="margin: 0;">+<span id="LC1822" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intStat</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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1823
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<pre style="margin: 0;">+<span id="LC1823" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" GTF file not found "</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;">gtfFile</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="new_line diff-line-num new" data-linenumber="1824" 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">
1824
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<pre style="margin: 0;">+<span id="LC1824" 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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1825
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<pre style="margin: 0;">+<span id="LC1825" class="line" lang="cpp"> <span class="p">}</span></span>
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1826
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<pre style="margin: 0;">+<span id="LC1826" class="line" lang="cpp"> <span class="p">}</span></span>
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1827
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<pre style="margin: 0;">+<span id="LC1827" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1828" 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">
1828
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<pre style="margin: 0;">+<span id="LC1828" 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;">genemap</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="new_line diff-line-num new" data-linenumber="1829" 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">
1829
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<pre style="margin: 0;">+<span id="LC1829" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1830" 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">
1830
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<pre style="margin: 0;">+<span id="LC1830" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intStat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">genemap</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1831" 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">
1831
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<pre style="margin: 0;">+<span id="LC1831" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intStat</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="new_line diff-line-num new" data-linenumber="1832" 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">
1832
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<pre style="margin: 0;">+<span id="LC1832" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file for mapping transcripts to genes not found "</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;">genemap</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="new_line diff-line-num new" data-linenumber="1833" 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">
1833
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<pre style="margin: 0;">+<span id="LC1833" 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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1834
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<pre style="margin: 0;">+<span id="LC1834" class="line" lang="cpp"> <span class="p">}</span></span>
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1835
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<pre style="margin: 0;">+<span id="LC1835" class="line" lang="cpp"> <span class="p">}</span></span>
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1836
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<pre style="margin: 0;">+<span id="LC1836" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1837" 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">
1837
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<pre style="margin: 0;">+<span id="LC1837" 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;">fld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</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;">fldFile</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="new_line diff-line-num new" data-linenumber="1838" 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">
1838
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<pre style="margin: 0;">+<span id="LC1838" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" cannot supply mean or sd while also supplying a fragment length distribution file"</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="new_line diff-line-num new" data-linenumber="1839" 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">
1839
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<pre style="margin: 0;">+<span id="LC1839" 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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1840
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<pre style="margin: 0;">+<span id="LC1840" class="line" lang="cpp"> <span class="p">}</span></span>
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1841
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<pre style="margin: 0;">+<span id="LC1841" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="1842" 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">
1842
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<pre style="margin: 0;">+<span id="LC1842" 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;">fld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fld</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span> <span class="p">{</span></span>
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1843
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<pre style="margin: 0;">+<span id="LC1843" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" cannot supply mean/sd without supplying both -l and -s"</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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1844
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<pre style="margin: 0;">+<span id="LC1844" 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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1845
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<pre style="margin: 0;">+<span id="LC1845" class="line" lang="cpp"> <span class="p">}</span></span>
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1846
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<pre style="margin: 0;">+<span id="LC1846" class="line" lang="cpp"> </span>
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1847
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<pre style="margin: 0;">+<span id="LC1847" 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;">index</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fldFile</span><span class="p">.</span><span class="n" style="color: #333;">empty</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;">fld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1848" 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">
1848
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<pre style="margin: 0;">+<span id="LC1848" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" cannot supply fragment length information unless a kallisto index is provided"</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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1849
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<pre style="margin: 0;">+<span id="LC1849" 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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1850
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<pre style="margin: 0;">+<span id="LC1850" class="line" lang="cpp"> <span class="p">}</span></span>
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1851
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<pre style="margin: 0;">+<span id="LC1851" class="line" lang="cpp"> </span>
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1852
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<pre style="margin: 0;">+<span id="LC1852" 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;">fld</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1853" 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">
1853
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<pre style="margin: 0;">+<span id="LC1853" 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;">"[tcc] fragment length distribution is truncated gaussian with mean = "</span> <span class="o" style="font-weight: 600;"><<</span></span>
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1854
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<pre style="margin: 0;">+<span id="LC1854" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fld</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", sd = "</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;">sd</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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1855
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<pre style="margin: 0;">+<span id="LC1855" class="line" lang="cpp"> <span class="p">}</span></span>
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1856
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<pre style="margin: 0;">+<span id="LC1856" class="line" lang="cpp"> </span>
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1857
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<pre style="margin: 0;">+<span id="LC1857" 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;">fld</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1858" 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">
1858
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<pre style="margin: 0;">+<span id="LC1858" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" invalid value for mean fragment length "</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;">fld</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="new_line diff-line-num new" data-linenumber="1859" 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">
1859
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<pre style="margin: 0;">+<span id="LC1859" 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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1860
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<pre style="margin: 0;">+<span id="LC1860" class="line" lang="cpp"> <span class="p">}</span></span>
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1861
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<pre style="margin: 0;">+<span id="LC1861" class="line" lang="cpp"> </span>
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1862
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<pre style="margin: 0;">+<span id="LC1862" 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;">sd</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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1863
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<pre style="margin: 0;">+<span id="LC1863" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" invalid value for fragment length standard deviation "</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;">sd</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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1864
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<pre style="margin: 0;">+<span id="LC1864" 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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1865
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<pre style="margin: 0;">+<span id="LC1865" class="line" lang="cpp"> <span class="p">}</span></span>
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1866
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<pre style="margin: 0;">+<span id="LC1866" class="line" lang="cpp"></span>
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1867
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<pre style="margin: 0;">+<span id="LC1867" 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;">output</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="new_line diff-line-num new" data-linenumber="1868" 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">
1868
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<pre style="margin: 0;">+<span id="LC1868" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" need to specify output directory "</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;">output</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="new_line diff-line-num new" data-linenumber="1869" 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">
1869
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<pre style="margin: 0;">+<span id="LC1869" 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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1870
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<pre style="margin: 0;">+<span id="LC1870" 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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1871
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<pre style="margin: 0;">+<span id="LC1871" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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1872
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<pre style="margin: 0;">+<span id="LC1872" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intStat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</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="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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1873
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<pre style="margin: 0;">+<span id="LC1873" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intStat</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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1874
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<pre style="margin: 0;">+<span id="LC1874" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// file/dir exits</span></span>
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1875
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<pre style="margin: 0;">+<span id="LC1875" 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;">S_ISDIR</span><span class="p">(</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">.</span><span class="n" style="color: #333;">st_mode</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1876" 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">
1876
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<pre style="margin: 0;">+<span id="LC1876" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file "</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;">output</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" exists and is not a directory"</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="new_line diff-line-num new" data-linenumber="1877" 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">
1877
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<pre style="margin: 0;">+<span id="LC1877" 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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1878
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<pre style="margin: 0;">+<span id="LC1878" class="line" lang="cpp"> <span class="p">}</span></span>
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1879
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<pre style="margin: 0;">+<span id="LC1879" 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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1880
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<pre style="margin: 0;">+<span id="LC1880" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// create directory</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1881" 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">
1881
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<pre style="margin: 0;">+<span id="LC1881" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">my_mkdir</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="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mo" style="color: #099;">0777</span><span class="p">)</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 class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1882" 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">
1882
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<pre style="margin: 0;">+<span id="LC1882" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" could not create directory "</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;">output</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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1883
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<pre style="margin: 0;">+<span id="LC1883" 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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1884
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<pre style="margin: 0;">+<span id="LC1884" class="line" lang="cpp"> <span class="p">}</span></span>
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1885
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<pre style="margin: 0;">+<span id="LC1885" class="line" lang="cpp"> <span class="p">}</span></span>
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1886
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<pre style="margin: 0;">+<span id="LC1886" class="line" lang="cpp"> <span class="p">}</span></span>
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1887
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<pre style="margin: 0;">+<span id="LC1887" class="line" lang="cpp"></span>
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1888
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<pre style="margin: 0;">+<span id="LC1888" 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;">threads</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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1889
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<pre style="margin: 0;">+<span id="LC1889" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" invalid number of threads "</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="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1890
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<pre style="margin: 0;">+<span id="LC1890" 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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1891
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<pre style="margin: 0;">+<span id="LC1891" 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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1892
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<pre style="margin: 0;">+<span id="LC1892" class="line" lang="cpp"> <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;">n</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;">hardware_concurrency</span><span class="p">();</span></span>
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1893
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<pre style="margin: 0;">+<span id="LC1893" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n</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;">n</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="p">{</span></span>
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1894
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<pre style="margin: 0;">+<span id="LC1894" 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: you asked for "</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>
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1895
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<pre style="margin: 0;">+<span id="LC1895" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", but only "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" cores on the machine"</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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1896
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<pre style="margin: 0;">+<span id="LC1896" class="line" lang="cpp"> <span class="p">}</span></span>
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1897
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<pre style="margin: 0;">+<span id="LC1897" class="line" lang="cpp"> <span class="p">}</span></span>
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1898
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<pre style="margin: 0;">+<span id="LC1898" class="line" lang="cpp"> </span>
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1289
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1899
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<pre style="margin: 0;"> <span id="LC1899" 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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1290
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1900
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<pre style="margin: 0;"> <span id="LC1900" 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 bootstrap samples must be a non-negative integer."</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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1291
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1901
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<pre style="margin: 0;"> <span id="LC1901" 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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1292
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1902
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<pre style="margin: 0;"> <span id="LC1902" class="line" lang="cpp"> <span class="p">}</span></span>
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1293
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1903
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<pre style="margin: 0;"> <span id="LC1903" class="line" lang="cpp"></span>
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1294
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<pre style="margin: 0;">-<span id="LC1294" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifndef USE_HDF5 </span></span>
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1295
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<pre style="margin: 0;">-<span id="LC1295" 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="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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1296
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<pre style="margin: 0;">-<span id="LC1296" 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: kallisto was not compiled with HDF5 support so no bootstrapping"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1297
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<pre style="margin: 0;">-<span id="LC1297" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"will be performed. Run quant with --plaintext option or recompile with"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1298
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<pre style="margin: 0;">-<span id="LC1298" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"HDF5 support to obtain bootstrap estimates."</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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1299
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<pre style="margin: 0;">-<span id="LC1299" class="line" lang="cpp"> <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>
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<pre style="margin: 0;">-<span id="LC1300" class="line" lang="cpp"> <span class="p">}</span></span>
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1301
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<pre style="margin: 0;">-<span id="LC1301" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC1302" 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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1904
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<pre style="margin: 0;">+<span id="LC1904" 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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1905
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<pre style="margin: 0;"> <span id="LC1905" class="line" lang="cpp"><span class="p">}</span></span>
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1906
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<pre style="margin: 0;"> <span id="LC1906" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1305" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1907" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">CheckOptionsMerge</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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1908
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<pre style="margin: 0;"> <span id="LC1908" class="line" lang="cpp"></span>
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1909
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<pre style="margin: 0;"> <span id="LC1909" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ret</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 unfold js-unfold old_line" data-linenumber="1404" style="width: 35px; color: rgba(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="2005" style="width: 35px; color: rgba(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">@@ -1404,12 +2005,24 @@ bool CheckOptionsPseudo(ProgramOptions& opt) {</td>
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1404
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2005
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<pre style="margin: 0;"> <span id="LC2005" 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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2006
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<pre style="margin: 0;"> <span id="LC2006" class="line" lang="cpp"> <span class="p">}</span></span>
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1406
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2007
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<pre style="margin: 0;"> <span id="LC2007" class="line" lang="cpp"> <span class="p">}</span></span>
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2008
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<pre style="margin: 0;">+<span id="LC2008" class="line" lang="cpp"> </span>
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2009
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<pre style="margin: 0;">+<span id="LC2009" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_bus</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;">batch_bus_write</span><span class="p">));</span></span>
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2010
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<pre style="margin: 0;">+<span id="LC2010" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">opt_bus_mode</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;">batch_bus</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;">batch_bus_write</span><span class="p">;</span></span>
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1407
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2011
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<pre style="margin: 0;"> <span id="LC2011" class="line" lang="cpp"></span>
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1408
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<td class="new_line diff-line-num" data-linenumber="2012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2012
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<pre style="margin: 0;"> <span id="LC2012" 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;">pseudo_quant</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1409
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2013
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<pre style="margin: 0;"> <span id="LC2013" 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;">batch_mode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1410
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2014
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<pre style="margin: 0;"> <span id="LC2014" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --quant can only be run with in batch mode with --batch"</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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1411
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2015
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<pre style="margin: 0;"> <span id="LC2015" 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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1412
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2016
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<pre style="margin: 0;"> <span id="LC2016" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2017" 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">
2017
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<pre style="margin: 0;">+<span id="LC2017" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_bus_mode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2018" 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">
2018
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<pre style="margin: 0;">+<span id="LC2018" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --quant cannot be run with --bus"</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="new_line diff-line-num new" data-linenumber="2019" 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">
2019
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<pre style="margin: 0;">+<span id="LC2019" 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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2020
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<pre style="margin: 0;">+<span id="LC2020" class="line" lang="cpp"> <span class="p">}</span></span>
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2021
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<pre style="margin: 0;">+<span id="LC2021" class="line" lang="cpp"> <span class="p">}</span></span>
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2022
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<pre style="margin: 0;">+<span id="LC2022" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="2023" 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">
2023
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<pre style="margin: 0;">+<span id="LC2023" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_bus_mode</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;">umi</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2024" 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">
2024
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<pre style="margin: 0;">+<span id="LC2024" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" UMI cannot be run with --bus"</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="new_line diff-line-num new" data-linenumber="2025" 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">
2025
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<pre style="margin: 0;">+<span id="LC2025" 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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1413
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<td class="new_line diff-line-num" data-linenumber="2026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2026
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<pre style="margin: 0;"> <span id="LC2026" class="line" lang="cpp"> <span class="p">}</span></span>
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1414
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<td class="new_line diff-line-num" data-linenumber="2027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2027
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<pre style="margin: 0;"> <span id="LC2027" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2028
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<pre style="margin: 0;"> <span id="LC2028" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check for read files</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1418" style="width: 35px; color: rgba(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="2031" style="width: 35px; color: rgba(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">@@ -1418,8 +2031,45 @@ bool CheckOptionsPseudo(ProgramOptions& opt) {</td>
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1418
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2031
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<pre style="margin: 0;"> <span id="LC2031" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" UMI must be run in batch mode, use --batch option"</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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1419
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<td class="new_line diff-line-num" data-linenumber="2032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2032
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<pre style="margin: 0;"> <span id="LC2032" 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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1420
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2033
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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="cpp"> <span class="p">}</span></span>
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1421
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<td class="new_line diff-line-num old" data-linenumber="2034" 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="LC1421" class="line" lang="cpp"> </span>
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1422
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<pre style="margin: 0;">-<span id="LC1422" 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;">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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2034" 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">
2034
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<pre style="margin: 0;">+<span id="LC2034" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_bus_mode</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ret</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2035" 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">
2035
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<pre style="margin: 0;">+<span id="LC2035" 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;">"--bus specified; will try running read files in batch mode"</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="new_line diff-line-num new" data-linenumber="2036" 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">
2036
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<pre style="margin: 0;">+<span id="LC2036" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_ids</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">"sample"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2037" 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">
2037
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<pre style="margin: 0;">+<span id="LC2037" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_mode</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="new_line diff-line-num new" data-linenumber="2038" 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">
2038
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<pre style="margin: 0;">+<span id="LC2038" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">pseudo_read_files_supplied</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="new_line diff-line-num new" data-linenumber="2039" 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">
2039
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<pre style="margin: 0;">+<span id="LC2039" 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;">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="mi" style="color: #099;">1</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="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2040" 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">
2040
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<pre style="margin: 0;">+<span id="LC2040" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" A minimum of one and a maximum of two read files must be provided"</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="new_line diff-line-num new" data-linenumber="2041" 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">
2041
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<pre style="margin: 0;">+<span id="LC2041" 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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<td class="new_line diff-line-num new" data-linenumber="2042" 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">
2042
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<pre style="margin: 0;">+<span id="LC2042" 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;">single_end</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="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2043" 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">
2043
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<pre style="margin: 0;">+<span id="LC2043" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" single-end mode requires exactly one read file"</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="new_line diff-line-num new" data-linenumber="2044" 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">
2044
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<pre style="margin: 0;">+<span id="LC2044" 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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<td class="new_line diff-line-num new" data-linenumber="2045" 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">
2045
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<pre style="margin: 0;">+<span id="LC2045" 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="new_line diff-line-num new" data-linenumber="2046" 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">
2046
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<pre style="margin: 0;">+<span id="LC2046" 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="n" style="color: #333;">f1</span><span class="p">,</span><span class="n" style="color: #333;">f2</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2047" 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">
2047
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<pre style="margin: 0;">+<span id="LC2047" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">stat</span> <span class="n" style="color: #333;">stFileInfo</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2048" 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">
2048
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<pre style="margin: 0;">+<span id="LC2048" 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;">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="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2049" 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">
2049
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<pre style="margin: 0;">+<span id="LC2049" class="line" lang="cpp"> <span class="n" style="color: #333;">f1</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="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2050" 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">
2050
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<pre style="margin: 0;">+<span id="LC2050" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">f1</span><span class="p">});</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2051" 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">
2051
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<pre style="margin: 0;">+<span id="LC2051" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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2052
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<pre style="margin: 0;">+<span id="LC2052" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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="new_line diff-line-num new" data-linenumber="2053" 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">
2053
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<pre style="margin: 0;">+<span id="LC2053" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">f1</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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2054
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<pre style="margin: 0;">+<span id="LC2054" 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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2055
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<pre style="margin: 0;">+<span id="LC2055" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2056" 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">
2056
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<pre style="margin: 0;">+<span id="LC2056" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2057" 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">
2057
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<pre style="margin: 0;">+<span id="LC2057" class="line" lang="cpp"> <span class="n" style="color: #333;">f1</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="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2058" 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">
2058
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<pre style="margin: 0;">+<span id="LC2058" class="line" lang="cpp"> <span class="n" style="color: #333;">f2</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="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2059" 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">
2059
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<pre style="margin: 0;">+<span id="LC2059" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_files</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">f1</span><span class="p">,</span><span class="n" style="color: #333;">f2</span><span class="p">});</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2060" 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">
2060
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<pre style="margin: 0;">+<span id="LC2060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">f1</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2061" 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">
2061
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<pre style="margin: 0;">+<span id="LC2061" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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="new_line diff-line-num new" data-linenumber="2062" 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">
2062
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<pre style="margin: 0;">+<span id="LC2062" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">f1</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="new_line diff-line-num new" data-linenumber="2063" 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">
2063
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<pre style="margin: 0;">+<span id="LC2063" 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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2064
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<pre style="margin: 0;">+<span id="LC2064" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2065" 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">
2065
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<pre style="margin: 0;">+<span id="LC2065" class="line" lang="cpp"> <span class="n" style="color: #333;">intstat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">stFileInfo</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2066" 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">
2066
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<pre style="margin: 0;">+<span id="LC2066" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intstat</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="new_line diff-line-num new" data-linenumber="2067" 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">
2067
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<pre style="margin: 0;">+<span id="LC2067" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" file not found "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">f2</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="new_line diff-line-num new" data-linenumber="2068" 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">
2068
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<pre style="margin: 0;">+<span id="LC2068" 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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<td class="new_line diff-line-num new" data-linenumber="2069" 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">
2069
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<pre style="margin: 0;">+<span id="LC2069" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="new_line diff-line-num new" 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="p">}</span></span>
</pre>
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<td class="new_line diff-line-num new" 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="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2072" 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">
2072
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<pre style="margin: 0;">+<span id="LC2072" 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;">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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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1423
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2073
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<pre style="margin: 0;"> <span id="LC2073" 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;">ERROR_STR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Missing read files"</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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1424
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2074
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<pre style="margin: 0;"> <span id="LC2074" 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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1425
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2075
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<pre style="margin: 0;"> <span id="LC2075" 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 unfold js-unfold old_line" data-linenumber="1511" style="width: 35px; color: rgba(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="2161" style="width: 35px; color: rgba(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">@@ -1511,6 +2161,12 @@ bool CheckOptionsPseudo(ProgramOptions& opt) {</td>
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1511
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2161
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<pre style="margin: 0;"> <span id="LC2161" 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;">fld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1512
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2162
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<pre style="margin: 0;"> <span id="LC2162" 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;">"[~warn] you supplied fragment length information for UMI data which 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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1513
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2163
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<pre style="margin: 0;"> <span id="LC2163" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2164" 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">
2164
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<pre style="margin: 0;">+<span id="LC2164" 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_bus_mode</span><span class="p">)</span> <span class="p">{</span></span>
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2165
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<pre style="margin: 0;">+<span id="LC2165" 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;">fld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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2166
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<pre style="margin: 0;">+<span id="LC2166" 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;">"[~warn] you supplied fragment length information for --bus mode which 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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2167
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<pre style="margin: 0;">+<span id="LC2167" class="line" lang="cpp"> <span class="p">}</span></span>
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2168
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<pre style="margin: 0;">+<span id="LC2168" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fld</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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2169
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<pre style="margin: 0;">+<span id="LC2169" class="line" lang="cpp"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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1514
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2170
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<pre style="margin: 0;"> <span id="LC2170" 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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1515
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2171
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<pre style="margin: 0;"> <span id="LC2171" 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;">fld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fld</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.0</span><span class="p">))</span> <span class="p">{</span></span>
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1516
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2172
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<pre style="margin: 0;"> <span id="LC2172" 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: cannot supply mean/sd without supplying both -l and -s"</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 unfold js-unfold old_line" data-linenumber="1585" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1585,6 +2241,25 @@ bool CheckOptionsPseudo(ProgramOptions& opt) {</td>
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1585
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2241
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<pre style="margin: 0;"> <span id="LC2241" 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: Pseudobam not supported yet in pseudo mode, use quant mode to obtain BAM files"</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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1586
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2242
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<pre style="margin: 0;"> <span id="LC2242" 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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1587
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2243
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<pre style="margin: 0;"> <span id="LC2243" class="line" lang="cpp"> <span class="p">}</span></span>
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2244
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<pre style="margin: 0;">+<span id="LC2244" class="line" lang="cpp"> </span>
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2245
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<pre style="margin: 0;">+<span id="LC2245" 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_bus_mode</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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2246
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<pre style="margin: 0;">+<span id="LC2246" 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: --bus option was not 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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2247
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<pre style="margin: 0;">+<span id="LC2247" class="line" lang="cpp"> <span class="p">}</span></span>
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2248
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<pre style="margin: 0;">+<span id="LC2248" class="line" lang="cpp"> </span>
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2249
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<pre style="margin: 0;">+<span id="LC2249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt_bus_mode</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ret</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Set up BUS options</span></span>
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2250
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<pre style="margin: 0;">+<span id="LC2250" 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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2251
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<pre style="margin: 0;">+<span id="LC2251" 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="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;">0</span><span class="p">));</span></span>
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2252
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<pre style="margin: 0;">+<span id="LC2252" 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="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2253
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<pre style="margin: 0;">+<span id="LC2253" 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;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2254
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<pre style="margin: 0;">+<span id="LC2254" 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;">single_end</span><span class="p">)</span> <span class="p">{</span></span>
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2255
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<pre style="margin: 0;">+<span id="LC2255" 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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2256
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<pre style="margin: 0;">+<span id="LC2256" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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2257
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<pre style="margin: 0;">+<span id="LC2257" 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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2258
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<pre style="margin: 0;">+<span id="LC2258" 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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2259
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<pre style="margin: 0;">+<span id="LC2259" 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="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;">0</span><span class="p">));</span></span>
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2260
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<pre style="margin: 0;">+<span id="LC2260" class="line" lang="cpp"> <span class="n" style="color: #333;">busopt</span><span class="p">.</span><span class="n" style="color: #333;">paired</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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2261
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<pre style="margin: 0;">+<span id="LC2261" class="line" lang="cpp"> <span class="p">}</span></span>
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2262
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<pre style="margin: 0;">+<span id="LC2262" class="line" lang="cpp"> <span class="p">}</span></span>
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1588
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2263
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<pre style="margin: 0;"> <span id="LC2263" class="line" lang="cpp"></span>
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1589
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2264
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<pre style="margin: 0;"> <span id="LC2264" 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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1590
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2265
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<pre style="margin: 0;"> <span id="LC2265" 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="1701" style="width: 35px; color: rgba(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="2376" style="width: 35px; color: rgba(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">@@ -1701,8 +2376,8 @@ void usage() {</td>
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1701
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2376
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<pre style="margin: 0;"> <span id="LC2376" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Where <CMD> can be one of:"</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="old_line diff-line-num" data-linenumber="1702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1702
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<td class="new_line diff-line-num" data-linenumber="2377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2377
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<pre style="margin: 0;"> <span id="LC2377" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" index Builds a kallisto index "</span><span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1703
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<td class="new_line diff-line-num" data-linenumber="2378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2378
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<pre style="margin: 0;"> <span id="LC2378" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" quant Runs the quantification algorithm "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2379" 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">
2379
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<pre style="margin: 0;">+<span id="LC2379" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" quant-tcc Runs quantification on transcript-compatibility counts"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="old_line diff-line-num" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1704
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<td class="new_line diff-line-num" data-linenumber="2380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2380
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<pre style="margin: 0;"> <span id="LC2380" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" bus Generate BUS files for single-cell data "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1705" 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">
1705
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<td class="new_line diff-line-num old" data-linenumber="2381" 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="LC1705" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" pseudo Runs the pseudoalignment step "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="old_line diff-line-num" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1706
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<td class="new_line diff-line-num" data-linenumber="2381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2381
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<pre style="margin: 0;"> <span id="LC2381" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" merge Merges several batch runs "</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="old_line diff-line-num" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1707
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<td class="new_line diff-line-num" data-linenumber="2382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2382
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<pre style="margin: 0;"> <span id="LC2382" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" h5dump Converts HDF5-formatted results to plaintext"</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="old_line diff-line-num" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1708
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<td class="new_line diff-line-num" data-linenumber="2383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2383
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<pre style="margin: 0;"> <span id="LC2383" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" inspect Inspects and gives information about an index"</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 unfold js-unfold old_line" data-linenumber="1718" style="width: 35px; color: rgba(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="2393" style="width: 35px; color: rgba(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">@@ -1718,13 +2393,24 @@ void usageBus() {</td>
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1718
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<td class="new_line diff-line-num" data-linenumber="2393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2393
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<pre style="margin: 0;"> <span id="LC2393" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Required arguments:"</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="old_line diff-line-num" data-linenumber="1719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1719
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<td class="new_line diff-line-num" data-linenumber="2394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2394
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<pre style="margin: 0;"> <span id="LC2394" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-i, --index=STRING Filename for the kallisto index to be used for"</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="old_line diff-line-num" data-linenumber="1720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1720
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<td class="new_line diff-line-num" data-linenumber="2395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2395
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<pre style="margin: 0;"> <span id="LC2395" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" pseudoalignment"</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="old_line diff-line-num old" data-linenumber="1721" 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">
1721
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<td class="new_line diff-line-num old" data-linenumber="2396" 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="LC1721" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-o, --output-dir=STRING Directory to write output to"</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="old_line diff-line-num old" data-linenumber="1722" 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">
1722
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<td class="new_line diff-line-num old" data-linenumber="2396" 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="LC1722" 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>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2396" 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">
2396
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<pre style="margin: 0;">+<span id="LC2396" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-o, --output-dir=STRING Directory to write output to"</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>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1723
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<td class="new_line diff-line-num" data-linenumber="2397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2397
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<pre style="margin: 0;"> <span id="LC2397" 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>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2398" 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">
2398
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<pre style="margin: 0;">+<span id="LC2398" 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>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1724
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<td class="new_line diff-line-num" data-linenumber="2399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2399
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<pre style="margin: 0;"> <span id="LC2399" 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="old_line diff-line-num new" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2400" 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">
2400
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<pre style="margin: 0;">+<span id="LC2400" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-B, --batch=FILE Process files listed in FILE"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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1725
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<td class="new_line diff-line-num" data-linenumber="2401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2401
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<pre style="margin: 0;"> <span id="LC2401" 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>
</pre>
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1726
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<td class="new_line diff-line-num" data-linenumber="2402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2402
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<pre style="margin: 0;"> <span id="LC2402" 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>
</pre>
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1727
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<td class="new_line diff-line-num" data-linenumber="2403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2403
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<pre style="margin: 0;"> <span id="LC2403" 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>
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<td class="new_line diff-line-num new" data-linenumber="2404" 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">
2404
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<pre style="margin: 0;">+<span id="LC2404" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-T, --tag=STRING 5′ tag sequence to identify UMI reads for certain technologies"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2405" 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">
2405
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<pre style="margin: 0;">+<span id="LC2405" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --fr-stranded Strand specific reads for UMI-tagged reads, first read forward"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2406" 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">
2406
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<pre style="margin: 0;">+<span id="LC2406" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --rf-stranded Strand specific reads for UMI-tagged reads, first read reverse"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2407" 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">
2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --unstranded Treat all read as non-strand-specific"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2408" 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">
2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --paired Treat reads as paired"</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="new_line diff-line-num new" data-linenumber="2409" 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">
2409
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<pre style="margin: 0;">+<span id="LC2409" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --genomebam Project pseudoalignments to genome sorted BAM file"</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="new_line diff-line-num new" data-linenumber="2410" 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">
2410
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<pre style="margin: 0;">+<span id="LC2410" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-g, --gtf GTF file for transcriptome information"</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="new_line diff-line-num new" data-linenumber="2411" 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">
2411
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<pre style="margin: 0;">+<span id="LC2411" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (required for --genomebam)"</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="new_line diff-line-num new" data-linenumber="2412" 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">
2412
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<pre style="margin: 0;">+<span id="LC2412" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-c, --chromosomes Tab separated file with chromosome names and lengths"</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="new_line diff-line-num new" data-linenumber="2413" 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">
2413
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<pre style="margin: 0;">+<span id="LC2413" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (optional for --genomebam, but recommended)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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1728
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<td class="new_line diff-line-num" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2414
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<pre style="margin: 0;"> <span id="LC2414" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --verbose Print out progress information every 1M proccessed reads"</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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1729
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2415
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<pre style="margin: 0;"> <span id="LC2415" class="line" lang="cpp"><span class="p">}</span></span>
</pre>
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1730
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<td class="new_line diff-line-num" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2416
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<pre style="margin: 0;"> <span id="LC2416" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1800" style="width: 35px; color: rgba(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="2486" style="width: 35px; color: rgba(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">@@ -1800,7 +2486,7 @@ void usageEM(bool valid_input = true) {</td>
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1800
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2486
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<pre style="margin: 0;"> <span id="LC2486" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">usagePseudo</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">valid_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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1801
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2487
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<pre style="margin: 0;"> <span id="LC2487" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid_input</span><span class="p">)</span> <span class="p">{</span></span>
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1802
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<td class="new_line diff-line-num" data-linenumber="2488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2488
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<pre style="margin: 0;"> <span id="LC2488" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"kallisto "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">KALLISTO_VERSION</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
</pre>
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1803
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<td class="new_line diff-line-num old" data-linenumber="2489" 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="LC1803" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Computes equivalence classes for reads and quantifies abundances"</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 class="p">;</span></span>
</pre>
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2489
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<pre style="margin: 0;">+<span id="LC2489" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Computes equivalence classes for reads and quantifies abundances<span class="idiff left right"> (deprecated)</span>"</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 class="p">;</span></span>
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1804
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2490
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<pre style="margin: 0;"> <span id="LC2490" class="line" lang="cpp"> <span class="p">}</span></span>
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1805
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2491
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<pre style="margin: 0;"> <span id="LC2491" class="line" lang="cpp"></span>
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1806
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2492
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<pre style="margin: 0;"> <span id="LC2492" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Usage: kallisto pseudo [arguments] FASTQ-files"</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 unfold js-unfold new_line" data-linenumber="2498" style="width: 35px; color: rgba(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">@@ -1812,11 +2498,16 @@ void usagePseudo(bool valid_input = true) {</td>
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1812
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2498
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<pre style="margin: 0;"> <span id="LC2498" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-u --umi First file in pair is a UMI file"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1813
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2499
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<pre style="margin: 0;"> <span id="LC2499" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-b --batch=FILE Process files listed in FILE"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1814
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2500
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<pre style="margin: 0;"> <span id="LC2500" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --quant Quantify using EM algorithm (only in batch mode)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2501
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<pre style="margin: 0;">+<span id="LC2501" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --bus Output a BUS file"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1815
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2502
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<pre style="margin: 0;"> <span id="LC2502" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --single Quantify single-end reads"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1816
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2503
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<pre style="margin: 0;"> <span id="LC2503" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-l, --fragment-length=DOUBLE Estimated average fragment length"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1817
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2504
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<pre style="margin: 0;"> <span id="LC2504" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-s, --sd=DOUBLE Estimated standard deviation of fragment length"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1818
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2505
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<pre style="margin: 0;"> <span id="LC2505" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (default: -l, -s values are estimated from paired"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1819
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<pre style="margin: 0;">-<span id="LC1819" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" end data, but are required when using --single)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2506
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<pre style="margin: 0;">+<span id="LC2506" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" end data, but are required when using --single"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2507
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<pre style="margin: 0;">+<span id="LC2507" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" unless outputting a BUS file via --bus)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2508
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<pre style="margin: 0;">+<span id="LC2508" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --fr-stranded Strand specific reads, first read forward"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2509
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<pre style="margin: 0;">+<span id="LC2509" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --rf-stranded Strand specific reads, first read reverse"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2510
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<pre style="margin: 0;">+<span id="LC2510" 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 BUS file flag column (only with --bus)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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1820
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2511
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<pre style="margin: 0;"> <span id="LC2511" 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>
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1821
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2512
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<pre style="margin: 0;"> <span id="LC2512" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// << " --pseudobam Output pseudoalignments in SAM format to stdout" << endl;</span></span>
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1822
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2513
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<pre style="margin: 0;"> <span id="LC2513" 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">@@ -1848,6 +2539,38 @@ void usageEMOnly() {</td>
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2539
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<pre style="margin: 0;"> <span id="LC2539" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --plaintext Output plaintext instead of HDF5"</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 class="p">;</span></span>
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1849
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2540
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<pre style="margin: 0;"> <span id="LC2540" class="line" lang="cpp"><span class="p">}</span></span>
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1850
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2541
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<pre style="margin: 0;"> <span id="LC2541" class="line" lang="cpp"></span>
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2542
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<pre style="margin: 0;">+<span id="LC2542" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">usageTCCQuant</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">valid_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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2543
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<pre style="margin: 0;">+<span id="LC2543" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid_input</span><span class="p">)</span> <span class="p">{</span></span>
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2544
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<pre style="margin: 0;">+<span id="LC2544" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"kallisto "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">KALLISTO_VERSION</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2545
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<pre style="margin: 0;">+<span id="LC2545" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Quantifies abundance from pre-computed transcript-compatibility counts"</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 class="p">;</span></span>
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2546
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<pre style="margin: 0;">+<span id="LC2546" class="line" lang="cpp"> <span class="p">}</span></span>
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2547
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<pre style="margin: 0;">+<span id="LC2547" class="line" lang="cpp"> </span>
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2548
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<pre style="margin: 0;">+<span id="LC2548" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Usage: kallisto quant-tcc [arguments] transcript-compatibility-counts-file"</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="new_line diff-line-num new" data-linenumber="2549" 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">
2549
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<pre style="margin: 0;">+<span id="LC2549" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Required arguments:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2550
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<pre style="margin: 0;">+<span id="LC2550" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-o, --output-dir=STRING Directory to write output to"</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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2551
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<pre style="margin: 0;">+<span id="LC2551" 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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2552
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<pre style="margin: 0;">+<span id="LC2552" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-i, --index=STRING Filename for the kallisto index to be used"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2553
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<pre style="margin: 0;">+<span id="LC2553" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (required if file with names of transcripts not supplied)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2554
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<pre style="margin: 0;">+<span id="LC2554" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-T, --txnames=STRING File with names of transcripts"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2555
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<pre style="margin: 0;">+<span id="LC2555" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (required if index file not supplied)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2556
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<pre style="margin: 0;">+<span id="LC2556" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-e, --ec-file=FILE File containing equivalence classes"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2557
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<pre style="margin: 0;">+<span id="LC2557" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (default: equivalence classes are taken from the index)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2558
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<pre style="margin: 0;">+<span id="LC2558" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-f, --fragment-file=FILE File containing fragment length distribution"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2559
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<pre style="margin: 0;">+<span id="LC2559" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (default: effective length normalization is not performed)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2560
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<pre style="margin: 0;">+<span id="LC2560" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-l, --fragment-length=DOUBLE Estimated average fragment length"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2561" 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">
2561
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<pre style="margin: 0;">+<span id="LC2561" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-s, --sd=DOUBLE Estimated standard deviation of fragment length"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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2562
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<pre style="margin: 0;">+<span id="LC2562" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (note: -l, -s values only should be supplied when"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2563" 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">
2563
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<pre style="margin: 0;">+<span id="LC2563" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" effective length normalization needs to be performed"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2564" 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">
2564
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<pre style="margin: 0;">+<span id="LC2564" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" but --fragment-file is not specified)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2565" 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">
2565
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<pre style="margin: 0;">+<span id="LC2565" 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="new_line diff-line-num new" data-linenumber="2566" 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">
2566
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<pre style="margin: 0;">+<span id="LC2566" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-g, --genemap File for mapping transcripts to genes"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2567" 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">
2567
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<pre style="margin: 0;">+<span id="LC2567" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (required for obtaining gene-level abundances)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2568" 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">
2568
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<pre style="margin: 0;">+<span id="LC2568" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-G, --gtf=FILE GTF file for transcriptome information"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2569" 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">
2569
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<pre style="margin: 0;">+<span id="LC2569" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (can be used instead of --genemap for obtaining gene-level abundances)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2570" 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">
2570
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<pre style="margin: 0;">+<span id="LC2570" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-b, --bootstrap-samples=INT Number of bootstrap samples (default: 0)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2571" 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">
2571
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<pre style="margin: 0;">+<span id="LC2571" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --seed=INT Seed for the bootstrap sampling (default: 42)"</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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2572
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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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1851
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2574
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<pre style="margin: 0;"> <span id="LC2574" 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="nf" style="color: #900; font-weight: 600;">argv_to_string</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="p">{</span></span>
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1852
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2575
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<pre style="margin: 0;"> <span id="LC2575" 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="n" style="color: #333;">res</span><span class="p">;</span></span>
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1853
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2576
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<pre style="margin: 0;"> <span id="LC2576" 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;">argc</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="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1929" style="width: 35px; color: rgba(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="2652" style="width: 35px; color: rgba(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">@@ -1929,7 +2652,115 @@ int main(int argc, char *argv[]) {</td>
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1929
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2652
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<pre style="margin: 0;"> <span id="LC2652" 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;">CheckOptionsBus</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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1930
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2653
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<pre style="margin: 0;"> <span id="LC2653" class="line" lang="cpp"> <span class="n" style="color: #333;">usageBus</span><span class="p">();</span></span>
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1931
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2654
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<pre style="margin: 0;"> <span id="LC2654" 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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1932
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<pre style="margin: 0;">-<span id="LC1932" 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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2655
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<pre style="margin: 0;">+<span id="LC2655" 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;">batch_mode</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// kallisto pseudo</span></span>
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2656
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<pre style="margin: 0;">+<span id="LC2656" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// pseudoalign the reads</span></span>
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2657
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<pre style="margin: 0;">+<span id="LC2657" class="line" lang="cpp"> <span class="n" style="color: #333;">KmerIndex</span> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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2658
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<pre style="margin: 0;">+<span id="LC2658" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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2659
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<pre style="margin: 0;">+<span id="LC2659" class="line" lang="cpp"> </span>
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2660
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<pre style="margin: 0;">+<span id="LC2660" class="line" lang="cpp"> <span class="n" style="color: #333;">MinCollector</span> <span class="n" style="color: #333;">collection</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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2661
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<pre style="margin: 0;">+<span id="LC2661" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">num_processed</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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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;">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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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;">int64_t</span> <span class="n" style="color: #333;">num_unique</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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2664
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<pre style="margin: 0;">+<span id="LC2664" class="line" lang="cpp"> </span>
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2665
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<pre style="margin: 0;">+<span id="LC2665" class="line" lang="cpp"> <span class="n" style="color: #333;">Transcriptome</span> <span class="n" style="color: #333;">model</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// empty model</span></span>
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2666
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<pre style="margin: 0;">+<span id="LC2666" 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;">gtfFile</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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2667
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<pre style="margin: 0;">+<span id="LC2667" class="line" lang="cpp"> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">parseGTF</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">gtfFile</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2668" 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">
2668
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<pre style="margin: 0;">+<span id="LC2668" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2669" 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">
2669
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<pre style="margin: 0;">+<span id="LC2669" class="line" lang="cpp"> <span class="n" style="color: #333;">MasterProcessor</span> <span class="n" style="color: #333;">MP</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2670" 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">
2670
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<pre style="margin: 0;">+<span id="LC2670" 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;">batch_mode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2671" 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">
2671
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<pre style="margin: 0;">+<span id="LC2671" class="line" lang="cpp"> <span class="n" style="color: #333;">num_processed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProcessReads</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>
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<td class="new_line diff-line-num new" data-linenumber="2672" 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">
2672
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<pre style="margin: 0;">+<span id="LC2672" class="line" lang="cpp"> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">write</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;">"/pseudoalignments"</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2673" 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">
2673
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<pre style="margin: 0;">+<span id="LC2673" 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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2674
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<pre style="margin: 0;">+<span id="LC2674" class="line" lang="cpp"> <span class="n" style="color: #333;">num_processed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ProcessBatchReads</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>
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2675
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<pre style="margin: 0;">+<span id="LC2675" class="line" lang="cpp"> <span class="p">}</span></span>
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2676
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<pre style="margin: 0;">+<span id="LC2676" class="line" lang="cpp"> </span>
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2677
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<pre style="margin: 0;">+<span id="LC2677" 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="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv_to_string</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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2678
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<pre style="margin: 0;">+<span id="LC2678" class="line" lang="cpp"> </span>
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2679
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<pre style="margin: 0;">+<span id="LC2679" 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;">batch_bus</span><span class="p">)</span> <span class="p">{</span></span>
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2680
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<pre style="margin: 0;">+<span id="LC2680" 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;">id</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;">id</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;">batchCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2681
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<pre style="margin: 0;">+<span id="LC2681" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cc</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;">batchCounts</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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2682
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<pre style="margin: 0;">+<span id="LC2682" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">cc</span><span class="p">)</span> <span class="p">{</span></span>
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2683
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<pre style="margin: 0;">+<span id="LC2683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">first</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="p">{</span></span>
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2684
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<pre style="margin: 0;">+<span id="LC2684" 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;">p</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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2685
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<pre style="margin: 0;">+<span id="LC2685" class="line" lang="cpp"> <span class="p">}</span></span>
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2686
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<pre style="margin: 0;">+<span id="LC2686" 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;">p</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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2687
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<pre style="margin: 0;">+<span id="LC2687" class="line" lang="cpp"> <span class="p">}</span></span>
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2688
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<pre style="margin: 0;">+<span id="LC2688" class="line" lang="cpp"> <span class="p">}</span></span>
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2689
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<pre style="margin: 0;">+<span id="LC2689" 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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2690
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<pre style="margin: 0;">+<span id="LC2690" 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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2691
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<pre style="margin: 0;">+<span id="LC2691" 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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2692
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<pre style="margin: 0;">+<span id="LC2692" class="line" lang="cpp"> <span class="p">}</span></span>
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2693
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<pre style="margin: 0;">+<span id="LC2693" 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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2694
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<pre style="margin: 0;">+<span id="LC2694" 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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2695
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<pre style="margin: 0;">+<span id="LC2695" class="line" lang="cpp"> <span class="p">}</span></span>
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2696
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<pre style="margin: 0;">+<span id="LC2696" class="line" lang="cpp"> <span class="p">}</span></span>
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2697
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<pre style="margin: 0;">+<span id="LC2697" class="line" lang="cpp"> </span>
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2698
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<pre style="margin: 0;">+<span id="LC2698" 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;">ofstream</span> <span class="n" style="color: #333;">transout_f</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;">"/transcripts.txt"</span><span class="p">));</span></span>
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2699
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<pre style="margin: 0;">+<span id="LC2699" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">target_names_</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2700" 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">
2700
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<pre style="margin: 0;">+<span id="LC2700" class="line" lang="cpp"> <span class="n" style="color: #333;">transout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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2701
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<pre style="margin: 0;">+<span id="LC2701" class="line" lang="cpp"> <span class="p">}</span></span>
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2702
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<pre style="margin: 0;">+<span id="LC2702" class="line" lang="cpp"> <span class="n" style="color: #333;">transout_f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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2703
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<pre style="margin: 0;">+<span id="LC2703" class="line" lang="cpp"> </span>
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2704
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<pre style="margin: 0;">+<span id="LC2704" class="line" lang="cpp"> <span class="n" style="color: #333;">plaintext_aux</span><span class="p">(</span></span>
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2705
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<pre style="margin: 0;">+<span id="LC2705" 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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2706
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<pre style="margin: 0;">+<span id="LC2706" 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="new_line diff-line-num new" data-linenumber="2707" 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">
2707
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<pre style="margin: 0;">+<span id="LC2707" 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="mi" style="color: #099;">0</span><span class="p">)),</span> <span class="c1" style="color: #998; font-style: italic;">// no bootstraps in pseudo</span></span>
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2708
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<pre style="margin: 0;">+<span id="LC2708" 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;">num_processed</span><span class="p">)),</span></span>
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2709
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<pre style="margin: 0;">+<span id="LC2709" 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;">num_pseudoaligned</span><span class="p">)),</span></span>
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2710
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<pre style="margin: 0;">+<span id="LC2710" 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;">num_unique</span><span class="p">)),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2711" 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">
2711
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<pre style="margin: 0;">+<span id="LC2711" class="line" lang="cpp"> <span class="n" style="color: #333;">KALLISTO_VERSION</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2712" 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">
2712
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<pre style="margin: 0;">+<span id="LC2712" 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;">INDEX_VERSION</span><span class="p">)),</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2713" 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">
2713
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<pre style="margin: 0;">+<span id="LC2713" class="line" lang="cpp"> <span class="n" style="color: #333;">start_time</span><span class="p">,</span></span>
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2714
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<pre style="margin: 0;">+<span id="LC2714" class="line" lang="cpp"> <span class="n" style="color: #333;">call</span><span class="p">);</span></span>
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2715
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<pre style="margin: 0;">+<span id="LC2715" class="line" lang="cpp"></span>
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2716
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<pre style="margin: 0;">+<span id="LC2716" 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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2717
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<pre style="margin: 0;">+<span id="LC2717" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="2718" 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">
2718
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<pre style="margin: 0;">+<span id="LC2718" 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="n" style="color: #333;">prefix</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;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/matrix"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2719" 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">
2719
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<pre style="margin: 0;">+<span id="LC2719" 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="n" style="color: #333;">ecfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".ec"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2720" 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">
2720
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<pre style="margin: 0;">+<span id="LC2720" 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="n" style="color: #333;">tccfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".tcc.mtx"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2721" 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">
2721
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<pre style="margin: 0;">+<span id="LC2721" 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="n" style="color: #333;">cellnamesfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".cells"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2722" 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">
2722
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<pre style="margin: 0;">+<span id="LC2722" 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="n" style="color: #333;">genelistname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".genelist.txt"</span><span class="p">;</span></span>
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2723
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<pre style="margin: 0;">+<span id="LC2723" 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="n" style="color: #333;">busbarcodelistname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".barcodes"</span><span class="p">;</span></span>
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2724
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<pre style="margin: 0;">+<span id="LC2724" 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="n" style="color: #333;">busoutputname</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;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/output.bus"</span><span class="p">;</span></span>
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2725
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<pre style="margin: 0;">+<span id="LC2725" class="line" lang="cpp"> </span>
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<td class="new_line diff-line-num new" data-linenumber="2726" 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">
2726
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<pre style="margin: 0;">+<span id="LC2726" class="line" lang="cpp"> <span class="n" style="color: #333;">writeECList</span><span class="p">(</span><span class="n" style="color: #333;">ecfilename</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2727" 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">
2727
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<pre style="margin: 0;">+<span id="LC2727" class="line" lang="cpp"> <span class="n" style="color: #333;">writeCellIds</span><span class="p">(</span><span class="n" style="color: #333;">cellnamesfilename</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_ids</span><span class="p">);</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2728" 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">
2728
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<pre style="margin: 0;">+<span id="LC2728" 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_bus</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;">batch_bus_write</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2729" 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">
2729
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<pre style="margin: 0;">+<span id="LC2729" 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_bus_write</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2730" 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">
2730
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<pre style="margin: 0;">+<span id="LC2730" class="line" lang="cpp"> <span class="n" style="color: #333;">writeBUSMatrix</span><span class="p">(</span><span class="n" style="color: #333;">busoutputname</span><span class="p">,</span> <span class="n" style="color: #333;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">ecmap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2731" 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">
2731
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<pre style="margin: 0;">+<span id="LC2731" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2732" 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">
2732
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<pre style="margin: 0;">+<span id="LC2732" 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;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="2733" 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">
2733
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<pre style="margin: 0;">+<span id="LC2733" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write out fake barcodes that identify each cell</span></span>
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2734
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<pre style="margin: 0;">+<span id="LC2734" 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;">fake_bcs</span><span class="p">;</span></span>
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2735
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<pre style="margin: 0;">+<span id="LC2735" class="line" lang="cpp"> <span class="n" style="color: #333;">fake_bcs</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</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;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</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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2737
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<pre style="margin: 0;">+<span id="LC2737" class="line" lang="cpp"> <span class="n" style="color: #333;">fake_bcs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">binaryToString</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">BUSFORMAT_FAKE_BARCODE_LEN</span><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 class="p">}</span></span>
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2739
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<pre style="margin: 0;">+<span id="LC2739" class="line" lang="cpp"> <span class="n" style="color: #333;">writeCellIds</span><span class="p">(</span><span class="n" style="color: #333;">busbarcodelistname</span><span class="p">,</span> <span class="n" style="color: #333;">fake_bcs</span><span class="p">);</span></span>
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2740
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<pre style="margin: 0;">+<span id="LC2740" class="line" lang="cpp"> <span class="p">}</span></span>
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2741
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<pre style="margin: 0;">+<span id="LC2741" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write out index:</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;">index</span><span class="p">.</span><span class="n" style="color: #333;">write</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;">"/index.saved"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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2743
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<pre style="margin: 0;">+<span id="LC2743" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write out fragment length distributions if reads paired-end:</span></span>
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2744
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<pre style="margin: 0;">+<span id="LC2744" 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;">single_end</span><span class="p">)</span> <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 class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">flensout_f</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;">"/flens.txt"</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="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">id</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;">id</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;">batch_ids</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2747
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<pre style="margin: 0;">+<span id="LC2747" 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;">fld</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;">batchFlens</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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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;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</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;">fld</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;">i</span> <span class="p">)</span> <span class="p">{</span></span>
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2749
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<pre style="margin: 0;">+<span id="LC2749" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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="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;">flensout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>
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2751
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<pre style="margin: 0;">+<span id="LC2751" class="line" lang="cpp"> <span class="p">}</span></span>
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2752
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<pre style="margin: 0;">+<span id="LC2752" class="line" lang="cpp"> <span class="n" style="color: #333;">flensout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">fld</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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2753
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<pre style="margin: 0;">+<span id="LC2753" class="line" lang="cpp"> <span class="p">}</span></span>
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2754
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<pre style="margin: 0;">+<span id="LC2754" class="line" lang="cpp"> <span class="n" style="color: #333;">flensout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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2755
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<pre style="margin: 0;">+<span id="LC2755" class="line" lang="cpp"> <span class="p">}</span></span>
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2756
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<pre style="margin: 0;">+<span id="LC2756" class="line" lang="cpp"> <span class="n" style="color: #333;">flensout_f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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2757
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<pre style="margin: 0;">+<span id="LC2757" class="line" lang="cpp"> <span class="p">}</span></span>
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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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2759
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<pre style="margin: 0;">+<span id="LC2759" 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;">gtfFile</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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2760
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<pre style="margin: 0;">+<span id="LC2760" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// write out gene info</span></span>
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2761
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<pre style="margin: 0;">+<span id="LC2761" class="line" lang="cpp"> <span class="n" style="color: #333;">writeGeneList</span><span class="p">(</span><span class="n" style="color: #333;">genelistname</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">);</span></span>
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2762
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<pre style="margin: 0;">+<span id="LC2762" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2763" 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">
2763
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<pre style="margin: 0;">+<span id="LC2763" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// kallisto bus -x</span></span>
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1933
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2764
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<pre style="margin: 0;"> <span id="LC2764" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_trans</span><span class="p">,</span> <span class="n" style="color: #333;">index_version</span><span class="p">;</span></span>
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1934
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2765
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<pre style="margin: 0;"> <span id="LC2765" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">num_processed</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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1935
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2766
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<pre style="margin: 0;"> <span id="LC2766" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2008" style="width: 35px; color: rgba(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="2839" style="width: 35px; color: rgba(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">@@ -2008,7 +2839,27 @@ int main(int argc, char *argv[]) {</td>
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2008
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2839
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<pre style="margin: 0;"> <span id="LC2839" class="line" lang="cpp"> <span class="n" style="color: #333;">transout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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2009
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2840
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<pre style="margin: 0;"> <span id="LC2840" class="line" lang="cpp"> <span class="p">}</span></span>
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2010
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<td class="new_line diff-line-num" data-linenumber="2841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2841
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<pre style="margin: 0;"> <span id="LC2841" class="line" lang="cpp"> <span class="n" style="color: #333;">transout_f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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2011
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<td class="new_line diff-line-num old" data-linenumber="2842" 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="LC2011" class="line" lang="cpp"></span>
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2842
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<pre style="margin: 0;">+<span id="LC2842" class="line" lang="cpp"> </span>
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2843
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<pre style="margin: 0;">+<span id="LC2843" 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;">fld</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2844" 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">
2844
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<pre style="margin: 0;">+<span id="LC2844" 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;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2845" 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">
2845
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<pre style="margin: 0;">+<span id="LC2845" class="line" lang="cpp"> <span class="n" style="color: #333;">fld</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;">flens</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// copy</span></span>
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2846
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<pre style="margin: 0;">+<span id="LC2846" class="line" lang="cpp"> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">compute_mean_frag_lens_trunc</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="c1" style="color: #998; font-style: italic;">// Write out index:</span></span>
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2848
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<pre style="margin: 0;">+<span id="LC2848" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">write</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;">"/index.saved"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">false</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;">// Write out fragment length distribution:</span></span>
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2850
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<pre style="margin: 0;">+<span id="LC2850" 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;">ofstream</span> <span class="n" style="color: #333;">flensout_f</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;">"/flens.txt"</span><span class="p">));</span></span>
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2851
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<pre style="margin: 0;">+<span id="LC2851" 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;">size_t</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;">fld</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;">i</span> <span class="p">)</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 class="k" style="font-weight: 600;">if</span> <span class="p">(</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="p">{</span></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;">flensout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</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="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;">flensout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">fld</span><span class="p">[</span><span class="n" style="color: #333;">i</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="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;">flensout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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 class="n" style="color: #333;">flensout_f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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2859
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<pre style="margin: 0;">+<span id="LC2859" 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;">busOptions</span><span class="p">.</span><span class="n" style="color: #333;">umi</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">fileno</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 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="c1" style="color: #998; font-style: italic;">// Write out index:</span></span>
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2861
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<pre style="margin: 0;">+<span id="LC2861" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">write</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;">"/index.saved"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">false</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="p">}</span></span>
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2012
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2863
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<pre style="margin: 0;"> <span id="LC2863" class="line" lang="cpp"></span>
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2013
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<td class="new_line diff-line-num" data-linenumber="2864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2864
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<pre style="margin: 0;"> <span id="LC2864" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// gather stats</span></span>
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2014
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2865
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<pre style="margin: 0;"> <span id="LC2865" class="line" lang="cpp"> <span class="n" style="color: #333;">num_unique</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="2395" style="width: 35px; color: rgba(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="3246" style="width: 35px; color: rgba(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">@@ -2395,6 +3246,302 @@ int main(int argc, char *argv[]) {</td>
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2395
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3246
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<pre style="margin: 0;"> <span id="LC3246" 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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2396
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3247
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<pre style="margin: 0;"> <span id="LC3247" class="line" lang="cpp"> <span class="p">}</span></span>
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2397
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3248
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<pre style="margin: 0;"> <span id="LC3248" class="line" lang="cpp"> <span class="p">}</span></span>
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3249
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<pre style="margin: 0;">+<span id="LC3249" 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-tcc"</span><span class="p">)</span> <span class="p">{</span></span>
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3250
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<pre style="margin: 0;">+<span id="LC3250" 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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3251
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<pre style="margin: 0;">+<span id="LC3251" class="line" lang="cpp"> <span class="n" style="color: #333;">usageTCCQuant</span><span class="p">();</span></span>
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3252
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<pre style="margin: 0;">+<span id="LC3252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3253
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<pre style="margin: 0;">+<span id="LC3253" class="line" lang="cpp"> <span class="p">}</span></span>
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3254
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<pre style="margin: 0;">+<span id="LC3254" class="line" lang="cpp"> <span class="n" style="color: #333;">ParseOptionsTCCQuant</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;">1</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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3255
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<pre style="margin: 0;">+<span id="LC3255" 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;">CheckOptionsTCCQuant</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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3256
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<pre style="margin: 0;">+<span id="LC3256" class="line" lang="cpp"> <span class="n" style="color: #333;">usageTCCQuant</span><span class="p">();</span></span>
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3257
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<pre style="margin: 0;">+<span id="LC3257" 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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3258
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<pre style="margin: 0;">+<span id="LC3258" 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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3259
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<pre style="margin: 0;">+<span id="LC3259" class="line" lang="cpp"> <span class="n" style="color: #333;">KmerIndex</span> <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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3260
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<pre style="margin: 0;">+<span id="LC3260" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// skip the k-mer map</span></span>
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3261
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<pre style="margin: 0;">+<span id="LC3261" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">num_ecs</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;">ecmap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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3262
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<pre style="margin: 0;">+<span id="LC3262" class="line" lang="cpp"> <span class="n" style="color: #333;">MinCollector</span> <span class="n" style="color: #333;">collection</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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3263
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<pre style="margin: 0;">+<span id="LC3263" 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="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="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333;">batchCounts</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Stores TCCs</span></span>
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3264
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<pre style="margin: 0;">+<span id="LC3264" 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;">ifstream</span> <span class="n" style="color: #333;">in</span><span class="p">((</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">tccFile</span><span class="p">));</span></span>
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3265
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<pre style="margin: 0;">+<span id="LC3265" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">firstline</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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3266
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<pre style="margin: 0;">+<span id="LC3266" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isMatrixFile</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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3267
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<pre style="margin: 0;">+<span id="LC3267" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">nrow</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;">ncol</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;">nlines</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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3268
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<pre style="margin: 0;">+<span id="LC3268" class="line" lang="cpp"> <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;">prevRow</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;">prevCol</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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3269
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<pre style="margin: 0;">+<span id="LC3269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Read in TCC file</span></span>
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3270
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<pre style="margin: 0;">+<span id="LC3270" 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="n" style="color: #333;">line</span><span class="p">;</span></span>
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3271
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<pre style="margin: 0;">+<span id="LC3271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">))</span> <span class="p">{</span></span>
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3272
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<pre style="margin: 0;">+<span id="LC3272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstline</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// First line decides whether the file is in matrix format</span></span>
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3273
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<pre style="margin: 0;">+<span id="LC3273" class="line" lang="cpp"> <span class="n" style="color: #333;">firstline</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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3274
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<pre style="margin: 0;">+<span id="LC3274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</span><span class="s" style="color: #d14;">"%%MatrixMarket"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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 class="p">{</span></span>
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3275
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<pre style="margin: 0;">+<span id="LC3275" 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;">"[tcc] Parsing transcript-compatibility counts (TCC) file as a matrix file"</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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3276
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<pre style="margin: 0;">+<span id="LC3276" class="line" lang="cpp"> <span class="n" style="color: #333;">isMatrixFile</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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3277
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<pre style="margin: 0;">+<span id="LC3277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</span><span class="s" style="color: #d14;">"%"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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 class="p">{</span> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// Skip header comments</span></span>
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3278
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<pre style="margin: 0;">+<span id="LC3278" 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;">stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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3279
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<pre style="margin: 0;">+<span id="LC3279" 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;">nrow</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">nlines</span><span class="p">;</span></span>
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3280
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<pre style="margin: 0;">+<span id="LC3280" 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;">"[tcc] Matrix dimensions: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pretty_num</span><span class="p">(</span><span class="n" style="color: #333;">nrow</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" x "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pretty_num</span><span class="p">(</span><span class="n" style="color: #333;">ncol</span><span class="p">)</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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3281
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<pre style="margin: 0;">+<span id="LC3281" class="line" lang="cpp"> <span class="n" style="color: #333;">batchCounts</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">nrow</span><span class="p">,</span> <span class="p">{});</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3282" 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">
3282
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<pre style="margin: 0;">+<span id="LC3282" 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="new_line diff-line-num new" data-linenumber="3283" 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">
3283
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<pre style="margin: 0;">+<span id="LC3283" 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;">"[tcc] Warning: Bootstrap can only be used for non-matrix files; will not be performed"</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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3284
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<pre style="margin: 0;">+<span id="LC3284" class="line" lang="cpp"> <span class="p">}</span></span>
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3285
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<pre style="margin: 0;">+<span id="LC3285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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3286
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<pre style="margin: 0;">+<span id="LC3286" 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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3287
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<pre style="margin: 0;">+<span id="LC3287" 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;">"[tcc] Transcript-compatibility counts (TCC) file is not in matrix format; "</span></span>
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3288
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<pre style="margin: 0;">+<span id="LC3288" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"it will not be parsed as a matrix file"</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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3289
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<pre style="margin: 0;">+<span id="LC3289" class="line" lang="cpp"> <span class="n" style="color: #333;">isMatrixFile</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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3290
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<pre style="margin: 0;">+<span id="LC3290" class="line" lang="cpp"> <span class="n" style="color: #333;">batchCounts</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="p">{});</span></span>
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3291
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<pre style="margin: 0;">+<span id="LC3291" class="line" lang="cpp"> <span class="p">}</span></span>
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3292
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<pre style="margin: 0;">+<span id="LC3292" class="line" lang="cpp"> <span class="p">}</span></span>
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3293
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<pre style="margin: 0;">+<span id="LC3293" 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;">stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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3294
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<pre style="margin: 0;">+<span id="LC3294" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">col</span><span class="p">,</span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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3295
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<pre style="margin: 0;">+<span id="LC3295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isMatrixFile</span><span class="p">)</span> <span class="p">{</span></span>
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3296
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<pre style="margin: 0;">+<span id="LC3296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">nlines</span><span class="p">)</span> <span class="p">{</span></span>
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3297
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<pre style="margin: 0;">+<span id="LC3297" 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;">"[tcc] Warning: TCC matrix file contains additional lines which will not be read; "</span></span>
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3298
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<pre style="margin: 0;">+<span id="LC3298" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"only "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pretty_num</span><span class="p">(</span><span class="n" style="color: #333;">nlines</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" entries, as specified on the first line, will be read."</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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3299
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<pre style="margin: 0;">+<span id="LC3299" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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3300
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<pre style="margin: 0;">+<span id="LC3300" class="line" lang="cpp"> <span class="p">}</span></span>
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3301
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<pre style="margin: 0;">+<span id="LC3301" 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;">row</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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3302
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<pre style="margin: 0;">+<span id="LC3302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nrow</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ncol</span><span class="p">)</span> <span class="p">{</span></span>
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3303
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<pre style="margin: 0;">+<span id="LC3303" 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;">"Error: TCC matrix file is malformed; "</span> </span>
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3304
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<pre style="margin: 0;">+<span id="LC3304" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"row numbers or column numbers exceed the dimensions of the matrix."</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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3305
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<pre style="margin: 0;">+<span id="LC3305" 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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3306
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<pre style="margin: 0;">+<span id="LC3306" class="line" lang="cpp"> <span class="p">}</span></span>
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3307
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<pre style="margin: 0;">+<span id="LC3307" 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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3308
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<pre style="margin: 0;">+<span id="LC3308" 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;">col</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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3309
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<pre style="margin: 0;">+<span id="LC3309" class="line" lang="cpp"> <span class="n" style="color: #333;">col</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;">// Because we'll consider non-matrix TCC files to be zero-indexed</span></span>
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3310
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<pre style="margin: 0;">+<span id="LC3310" class="line" lang="cpp"> <span class="n" style="color: #333;">row</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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3311
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<pre style="margin: 0;">+<span id="LC3311" class="line" lang="cpp"> <span class="n" style="color: #333;">nrow</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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3312
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<pre style="margin: 0;">+<span id="LC3312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">col</span><span class="p">)</span> <span class="p">{</span></span>
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3313
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<pre style="margin: 0;">+<span id="LC3313" class="line" lang="cpp"> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">col</span><span class="p">;</span></span>
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3314
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<pre style="margin: 0;">+<span id="LC3314" class="line" lang="cpp"> <span class="p">}</span></span>
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3315
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<pre style="margin: 0;">+<span id="LC3315" class="line" lang="cpp"> <span class="p">}</span></span>
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3316
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<pre style="margin: 0;">+<span id="LC3316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">row</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;">col</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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3317
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<pre style="margin: 0;">+<span id="LC3317" 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;">"Error: Invalid indices in TCC file."</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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3318
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<pre style="margin: 0;">+<span id="LC3318" 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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3319
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<pre style="margin: 0;">+<span id="LC3319" class="line" lang="cpp"> <span class="p">}</span></span>
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3320
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<pre style="margin: 0;">+<span id="LC3320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">prevRow</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">prevRow</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">col</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">prevCol</span><span class="p">))</span> <span class="p">{</span></span>
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3321
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<pre style="margin: 0;">+<span id="LC3321" 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;">"Error: TCC file is not sorted."</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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3322
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<pre style="margin: 0;">+<span id="LC3322" 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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3323
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<pre style="margin: 0;">+<span id="LC3323" class="line" lang="cpp"> <span class="p">}</span></span>
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3324
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<pre style="margin: 0;">+<span id="LC3324" class="line" lang="cpp"> <span class="n" style="color: #333;">prevRow</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">;</span></span>
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3325
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<pre style="margin: 0;">+<span id="LC3325" class="line" lang="cpp"> <span class="n" style="color: #333;">prevCol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">col</span><span class="p">;</span></span>
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3326
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<pre style="margin: 0;">+<span id="LC3326" 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;">bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">batchCounts</span><span class="p">[</span><span class="n" style="color: #333;">row</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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3327
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<pre style="margin: 0;">+<span id="LC3327" class="line" lang="cpp"> <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;">col</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">val</span><span class="p">});</span></span>
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3328
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<pre style="margin: 0;">+<span id="LC3328" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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3329
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<pre style="margin: 0;">+<span id="LC3329" class="line" lang="cpp"> <span class="p">}</span></span>
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3330
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<pre style="margin: 0;">+<span id="LC3330" 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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3331
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<pre style="margin: 0;">+<span id="LC3331" 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;">"Error: could not open file "</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;">tccFile</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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3332
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<pre style="margin: 0;">+<span id="LC3332" 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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3333
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<pre style="margin: 0;">+<span id="LC3333" class="line" lang="cpp"> <span class="p">}</span></span>
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3334
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<pre style="margin: 0;">+<span id="LC3334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isMatrixFile</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nlines</span><span class="p">)</span> <span class="p">{</span></span>
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3335
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<pre style="margin: 0;">+<span id="LC3335" 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;">"Error: Found only "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pretty_num</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="s" style="color: #d14;">" entries in TCC matrix file, "</span></span>
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3336
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<pre style="margin: 0;">+<span id="LC3336" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"expected "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pretty_num</span><span class="p">(</span><span class="n" style="color: #333;">nlines</span><span class="p">)</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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3337
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<pre style="margin: 0;">+<span id="LC3337" 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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3338
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<pre style="margin: 0;">+<span id="LC3338" class="line" lang="cpp"> <span class="p">}</span></span>
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3339
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<pre style="margin: 0;">+<span id="LC3339" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">isMatrixFile</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">num_ecs</span><span class="p">)</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;">isMatrixFile</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ncol</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">num_ecs</span><span class="p">))</span> <span class="p">{</span></span>
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3340
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<pre style="margin: 0;">+<span id="LC3340" 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;">"Error: number of equivalence classes does not match index. Found "</span></span>
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3341
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<pre style="margin: 0;">+<span id="LC3341" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pretty_num</span><span class="p">(</span><span class="n" style="color: #333;">ncol</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">", expected "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pretty_num</span><span class="p">(</span><span class="n" style="color: #333;">num_ecs</span><span class="p">)</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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3342
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<pre style="margin: 0;">+<span id="LC3342" 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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3343
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<pre style="margin: 0;">+<span id="LC3343" class="line" lang="cpp"> <span class="p">}</span></span>
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3344
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<pre style="margin: 0;">+<span id="LC3344" class="line" lang="cpp"> </span>
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3345
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<pre style="margin: 0;">+<span id="LC3345" 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="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="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>>></span> <span class="n" style="color: #333;">Abundance_mat</span><span class="p">,</span> <span class="n" style="color: #333;">Abundance_mat_gene</span><span class="p">,</span> <span class="n" style="color: #333;">TPM_mat</span><span class="p">,</span> <span class="n" style="color: #333;">TPM_mat_gene</span><span class="p">;</span></span>
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3346
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<pre style="margin: 0;">+<span id="LC3346" class="line" lang="cpp"> <span class="n" style="color: #333;">Abundance_mat</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nrow</span><span class="p">,</span> <span class="p">{});</span></span>
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3347
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<pre style="margin: 0;">+<span id="LC3347" class="line" lang="cpp"> <span class="n" style="color: #333;">Abundance_mat_gene</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nrow</span><span class="p">,</span> <span class="p">{});</span></span>
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3348
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<pre style="margin: 0;">+<span id="LC3348" class="line" lang="cpp"> <span class="n" style="color: #333;">TPM_mat</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nrow</span><span class="p">,</span> <span class="p">{});</span></span>
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3349
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<pre style="margin: 0;">+<span id="LC3349" class="line" lang="cpp"> <span class="n" style="color: #333;">TPM_mat_gene</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nrow</span><span class="p">,</span> <span class="p">{});</span></span>
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3350
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<pre style="margin: 0;">+<span id="LC3350" 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="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">FLD_mat</span><span class="p">;</span></span>
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3351
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<pre style="margin: 0;">+<span id="LC3351" class="line" lang="cpp"> <span class="n" style="color: #333;">FLD_mat</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">nrow</span><span class="p">,</span> <span class="p">{});</span></span>
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3352
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<pre style="margin: 0;">+<span id="LC3352" 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;">FLDs</span><span class="p">;</span></span>
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3353
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<pre style="margin: 0;">+<span id="LC3353" class="line" lang="cpp"> <span class="n" style="color: #333;">Transcriptome</span> <span class="n" style="color: #333;">model</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// empty model</span></span>
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3354
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<pre style="margin: 0;">+<span id="LC3354" class="line" lang="cpp"></span>
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3355
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<pre style="margin: 0;">+<span id="LC3355" 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;">ofstream</span> <span class="n" style="color: #333;">transout_f</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;">"/transcripts.txt"</span><span class="p">));</span></span>
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3356
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<pre style="margin: 0;">+<span id="LC3356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">target_names_</span><span class="p">)</span> <span class="p">{</span></span>
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3357
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<pre style="margin: 0;">+<span id="LC3357" class="line" lang="cpp"> <span class="n" style="color: #333;">transout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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3358
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<pre style="margin: 0;">+<span id="LC3358" class="line" lang="cpp"> <span class="p">}</span></span>
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3359
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<pre style="margin: 0;">+<span id="LC3359" class="line" lang="cpp"> <span class="n" style="color: #333;">transout_f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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3360
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<pre style="margin: 0;">+<span id="LC3360" 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="n" style="color: #333;">prefix</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;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/matrix"</span><span class="p">;</span></span>
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3361
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<pre style="margin: 0;">+<span id="LC3361" 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="n" style="color: #333;">abtsvfilename</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;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/abundance.tsv"</span><span class="p">;</span></span>
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3362
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<pre style="margin: 0;">+<span id="LC3362" 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="n" style="color: #333;">gene_abtsvfilename</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;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/abundance.gene.tsv"</span><span class="p">;</span></span>
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3363
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<pre style="margin: 0;">+<span id="LC3363" 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="n" style="color: #333;">genelistname</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;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/genes.txt"</span><span class="p">;</span></span>
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3364
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<pre style="margin: 0;">+<span id="LC3364" 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="n" style="color: #333;">abfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".abundance.mtx"</span><span class="p">;</span></span>
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3365
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<pre style="margin: 0;">+<span id="LC3365" 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="n" style="color: #333;">abtpmfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".abundance.tpm.mtx"</span><span class="p">;</span></span>
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3366
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<pre style="margin: 0;">+<span id="LC3366" 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="n" style="color: #333;">gene_abfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".abundance.gene.mtx"</span><span class="p">;</span></span>
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3367
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<pre style="margin: 0;">+<span id="LC3367" 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="n" style="color: #333;">gene_abtpmfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".abundance.gene.tpm.mtx"</span><span class="p">;</span></span>
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3368
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<pre style="margin: 0;">+<span id="LC3368" 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="n" style="color: #333;">fldfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fld.tsv"</span><span class="p">;</span></span>
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3369
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<pre style="margin: 0;">+<span id="LC3369" class="line" lang="cpp"></span>
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3370
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<pre style="margin: 0;">+<span id="LC3370" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">calcEffLen</span> <span class="o" style="font-weight: 600;">=</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;">fldFile</span><span class="p">.</span><span class="n" style="color: #333;">empty</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;">fld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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3371
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<pre style="margin: 0;">+<span id="LC3371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">calcEffLen</span> <span class="o" style="font-weight: 600;">&&</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;">fldFile</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Parse supplied fragment length distribution file</span></span>
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3372
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<pre style="margin: 0;">+<span id="LC3372" 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;">ifstream</span> <span class="n" style="color: #333;">infld</span><span class="p">((</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fldFile</span><span class="p">));</span></span>
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3373
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<pre style="margin: 0;">+<span id="LC3373" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">infld</span><span class="p">.</span><span class="n" style="color: #333;">is_open</span><span class="p">())</span> <span class="p">{</span></span>
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3374
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<pre style="margin: 0;">+<span id="LC3374" 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="n" style="color: #333;">line</span><span class="p">;</span></span>
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3375
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<pre style="margin: 0;">+<span id="LC3375" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">infld</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">))</span> <span class="p">{</span></span>
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3376
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<pre style="margin: 0;">+<span id="LC3376" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</span><span class="s" style="color: #d14;">"#"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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 class="p">{</span></span>
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3377
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<pre style="margin: 0;">+<span id="LC3377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Ignore empty lines or lines that begin with a #</span></span>
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3378
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<pre style="margin: 0;">+<span id="LC3378" class="line" lang="cpp"> <span class="p">}</span></span>
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3379
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<pre style="margin: 0;">+<span id="LC3379" 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;">tmp_vec</span><span class="p">;</span></span>
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3380
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<pre style="margin: 0;">+<span id="LC3380" 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;">stringstream</span> <span class="n" style="color: #333;">ss</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">);</span></span>
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3381
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<pre style="margin: 0;">+<span id="LC3381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">ss</span><span class="p">.</span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span></span>
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3382
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<pre style="margin: 0;">+<span id="LC3382" 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="n" style="color: #333;">tmp_val</span><span class="p">;</span></span>
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3383
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<pre style="margin: 0;">+<span id="LC3383" class="line" lang="cpp"> <span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">ss</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_val</span><span class="p">,</span> <span class="sc" style="color: #d14;">' '</span><span class="p">);</span></span>
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3384
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<pre style="margin: 0;">+<span id="LC3384" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmp_val_num</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;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">tmp_val</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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3385
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<pre style="margin: 0;">+<span id="LC3385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmp_val_num</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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3386
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<pre style="margin: 0;">+<span id="LC3386" 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;">"Error: Fragment length distribution file contains invalid value: "</span> </span>
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3387
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<pre style="margin: 0;">+<span id="LC3387" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tmp_val_num</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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3388
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<pre style="margin: 0;">+<span id="LC3388" 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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3389
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<pre style="margin: 0;">+<span id="LC3389" class="line" lang="cpp"> <span class="p">}</span></span>
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3390
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<pre style="margin: 0;">+<span id="LC3390" class="line" lang="cpp"> <span class="n" style="color: #333;">tmp_vec</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp_val_num</span><span class="p">);</span></span>
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3391
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<pre style="margin: 0;">+<span id="LC3391" class="line" lang="cpp"> <span class="p">}</span></span>
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3392
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<pre style="margin: 0;">+<span id="LC3392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tmp_vec</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;">MAX_FRAG_LEN</span><span class="p">)</span> <span class="p">{</span></span>
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3393
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<pre style="margin: 0;">+<span id="LC3393" 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;">"Error: Fragment length distribution file contains a line with "</span> </span>
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3394
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<pre style="margin: 0;">+<span id="LC3394" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tmp_vec</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;">" values; expected: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">MAX_FRAG_LEN</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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3395
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<pre style="margin: 0;">+<span id="LC3395" 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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3396
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<pre style="margin: 0;">+<span id="LC3396" class="line" lang="cpp"> <span class="p">}</span></span>
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3397
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<pre style="margin: 0;">+<span id="LC3397" class="line" lang="cpp"> <span class="n" style="color: #333;">FLDs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tmp_vec</span><span class="p">);</span></span>
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3398
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<pre style="margin: 0;">+<span id="LC3398" class="line" lang="cpp"> <span class="p">}</span></span>
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3399
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<pre style="margin: 0;">+<span id="LC3399" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">FLDs</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;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">FLDs</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;">nrow</span><span class="p">)</span> <span class="p">{</span></span>
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3400
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<pre style="margin: 0;">+<span id="LC3400" 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;">"Error: Fragment length distribution file contains "</span> </span>
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3401
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<pre style="margin: 0;">+<span id="LC3401" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">FLDs</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;">" valid lines; expected: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nrow</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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3402
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<pre style="margin: 0;">+<span id="LC3402" 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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3403
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<pre style="margin: 0;">+<span id="LC3403" class="line" lang="cpp"> <span class="p">}</span></span>
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3404
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<pre style="margin: 0;">+<span id="LC3404" 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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3405
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<pre style="margin: 0;">+<span id="LC3405" 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;">"Error: could not open file "</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;">fldFile</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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3406
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<pre style="margin: 0;">+<span id="LC3406" 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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3407
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<pre style="margin: 0;">+<span id="LC3407" class="line" lang="cpp"> <span class="p">}</span></span>
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3408
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<pre style="margin: 0;">+<span id="LC3408" class="line" lang="cpp"> <span class="p">}</span></span>
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3409
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<pre style="margin: 0;">+<span id="LC3409" class="line" lang="cpp"></span>
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3410
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<pre style="margin: 0;">+<span id="LC3410" 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;">genemap</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Parse supplied gene mapping file</span></span>
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3411
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<pre style="margin: 0;">+<span id="LC3411" class="line" lang="cpp"> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">parseGeneMap</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">genemap</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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3412
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<pre style="margin: 0;">+<span id="LC3412" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">gtfFile</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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3413
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<pre style="margin: 0;">+<span id="LC3413" class="line" lang="cpp"> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">parseGTF</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">gtfFile</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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3414
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<pre style="margin: 0;">+<span id="LC3414" class="line" lang="cpp"> <span class="p">}</span></span>
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3415
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<pre style="margin: 0;">+<span id="LC3415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">gene_level_counting</span> <span class="o" style="font-weight: 600;">=</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;">genemap</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</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;">gtfFile</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>
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3416
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<pre style="margin: 0;">+<span id="LC3416" class="line" lang="cpp"></span>
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3417
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<pre style="margin: 0;">+<span id="LC3417" 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;">"[quant] Running EM algorithm..."</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;">cerr</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3418" 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">
3418
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<pre style="margin: 0;">+<span id="LC3418" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">EM_lambda</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</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="n" style="color: #333;">id</span><span class="p">)</span> <span class="p">{</span></span>
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3419
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<pre style="margin: 0;">+<span id="LC3419" class="line" lang="cpp"> <span class="n" style="color: #333;">MinCollector</span> <span class="n" style="color: #333;">collection</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3420" 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">
3420
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<pre style="margin: 0;">+<span id="LC3420" class="line" lang="cpp"> <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;">assign</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">ecmap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3421
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<pre style="margin: 0;">+<span id="LC3421" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">batchCounts</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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3422
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<pre style="margin: 0;">+<span id="LC3422" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">bc</span><span class="p">)</span> <span class="p">{</span></span>
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3423
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<pre style="margin: 0;">+<span id="LC3423" class="line" lang="cpp"> <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;">p</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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3424
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<pre style="margin: 0;">+<span id="LC3424" class="line" lang="cpp"> <span class="p">}</span></span>
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3425
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<pre style="margin: 0;">+<span id="LC3425" class="line" lang="cpp"> </span>
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3426
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<pre style="margin: 0;">+<span id="LC3426" 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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fl_means</span><span class="p">;</span></span>
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3427
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<pre style="margin: 0;">+<span id="LC3427" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">calcEffLen</span><span class="p">)</span> <span class="p">{</span></span>
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3428
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<pre style="margin: 0;">+<span id="LC3428" 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;">fld</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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3429
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<pre style="margin: 0;">+<span id="LC3429" class="line" lang="cpp"> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">init_mean_fl_trunc</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">fld</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">sd</span><span class="p">);</span></span>
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3430
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<pre style="margin: 0;">+<span id="LC3430" 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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3431
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<pre style="margin: 0;">+<span id="LC3431" 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;">fld</span><span class="p">;</span></span>
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3432
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<pre style="margin: 0;">+<span id="LC3432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">FLDs</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;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Only one distribution supplied; will use this for everything</span></span>
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3433
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<pre style="margin: 0;">+<span id="LC3433" class="line" lang="cpp"> <span class="n" style="color: #333;">fld</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FLDs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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3434
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<pre style="margin: 0;">+<span id="LC3434" 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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3435
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<pre style="margin: 0;">+<span id="LC3435" class="line" lang="cpp"> <span class="n" style="color: #333;">fld</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FLDs</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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3436
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<pre style="margin: 0;">+<span id="LC3436" class="line" lang="cpp"> <span class="p">}</span></span>
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3437
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<pre style="margin: 0;">+<span id="LC3437" class="line" lang="cpp"> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">flens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fld</span><span class="p">;</span></span>
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3438
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<pre style="margin: 0;">+<span id="LC3438" class="line" lang="cpp"> <span class="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">compute_mean_frag_lens_trunc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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3439
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<pre style="margin: 0;">+<span id="LC3439" class="line" lang="cpp"> <span class="p">}</span></span>
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3440
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<pre style="margin: 0;">+<span id="LC3440" class="line" lang="cpp"> <span class="n" style="color: #333;">fl_means</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_frag_len_means</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="n" style="color: #333;">collection</span><span class="p">.</span><span class="n" style="color: #333;">mean_fl_trunc</span><span class="p">);</span></span>
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3441
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<pre style="margin: 0;">+<span id="LC3441" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean_fl</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;">get_mean_frag_len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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3442
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<pre style="margin: 0;">+<span id="LC3442" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sd_fl</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;">get_sd_frag_len</span><span class="p">();</span></span>
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3443
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<pre style="margin: 0;">+<span id="LC3443" class="line" lang="cpp"> <span class="n" style="color: #333;">FLD_mat</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">mean_fl</span><span class="p">,</span> <span class="n" style="color: #333;">sd_fl</span><span class="p">};</span></span>
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3444
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<pre style="margin: 0;">+<span id="LC3444" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Set mean fragment lengths to be target lengths so that effective lengths are all one</span></span>
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<pre style="margin: 0;">+<span id="LC3445" class="line" lang="cpp"> <span class="n" style="color: #333;">fl_means</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;">double</span><span class="o" style="font-weight: 600;">></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="n" style="color: #333;">begin</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="n" style="color: #333;">end</span><span class="p">());</span></span>
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3446
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<pre style="margin: 0;">+<span id="LC3446" class="line" lang="cpp"> <span class="p">}</span></span>
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3447
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<pre style="margin: 0;">+<span id="LC3447" class="line" lang="cpp"></span>
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3448
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<pre style="margin: 0;">+<span id="LC3448" class="line" lang="cpp"> <span class="n" style="color: #333;">EMAlgorithm</span> <span class="n" style="color: #333;">em</span><span class="p">(</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;">index</span><span class="p">,</span> <span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="n" style="color: #333;">fl_means</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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3449
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<pre style="margin: 0;">+<span id="LC3449" class="line" lang="cpp"> <span class="n" style="color: #333;">em</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">(</span><span class="mi" style="color: #099;">10000</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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3450
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<pre style="margin: 0;">+<span id="LC3450" class="line" lang="cpp"> </span>
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3451
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<pre style="margin: 0;">+<span id="LC3451" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isMatrixFile</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Update abundances matrix</span></span>
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3452
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<pre style="margin: 0;">+<span id="LC3452" 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;">ab_m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Abundance_mat</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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3453
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<pre style="margin: 0;">+<span id="LC3453" 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;">tpm_m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TPM_mat</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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3454
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<pre style="margin: 0;">+<span id="LC3454" 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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gc</span><span class="p">;</span></span>
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3455
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<pre style="margin: 0;">+<span id="LC3455" 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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">gc_tpm</span><span class="p">;</span></span>
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3456
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<pre style="margin: 0;">+<span id="LC3456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gene_level_counting</span><span class="p">)</span> <span class="p">{</span></span>
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3457
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<pre style="margin: 0;">+<span id="LC3457" class="line" lang="cpp"> <span class="n" style="color: #333;">gc</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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3458
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<pre style="margin: 0;">+<span id="LC3458" class="line" lang="cpp"> <span class="n" style="color: #333;">gc_tpm</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mf" style="color: #099;">0.0</span><span class="p">);</span></span>
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3459
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<pre style="margin: 0;">+<span id="LC3459" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC3460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">tpm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">counts_to_tpm</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>
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3461
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<pre style="margin: 0;">+<span id="LC3461" 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;">em</span><span class="p">.</span><span class="n" style="color: #333;">alpha_</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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3462
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<pre style="margin: 0;">+<span id="LC3462" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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3463
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<pre style="margin: 0;">+<span id="LC3463" class="line" lang="cpp"> <span class="n" style="color: #333;">ab_m</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">i</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;">i</span><span class="p">]});</span></span>
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3464
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<pre style="margin: 0;">+<span id="LC3464" class="line" lang="cpp"> <span class="n" style="color: #333;">tpm_m</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">tpm</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]});</span></span>
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3465
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<pre style="margin: 0;">+<span id="LC3465" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gene_level_counting</span><span class="p">)</span> <span class="p">{</span></span>
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3466
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<pre style="margin: 0;">+<span id="LC3466" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">g_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">transcripts</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">gene_id</span><span class="p">;</span></span>
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3467
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<pre style="margin: 0;">+<span id="LC3467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g_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 class="p">{</span></span>
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3468
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<pre style="margin: 0;">+<span id="LC3468" class="line" lang="cpp"> <span class="n" style="color: #333;">gc</span><span class="p">[</span><span class="n" style="color: #333;">g_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</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;">i</span><span class="p">];</span></span>
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3469
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<pre style="margin: 0;">+<span id="LC3469" class="line" lang="cpp"> <span class="n" style="color: #333;">gc_tpm</span><span class="p">[</span><span class="n" style="color: #333;">g_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tpm</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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3470
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<pre style="margin: 0;">+<span id="LC3470" class="line" lang="cpp"> <span class="p">}</span></span>
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3471
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<pre style="margin: 0;">+<span id="LC3471" class="line" lang="cpp"> <span class="p">}</span></span>
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3472
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<pre style="margin: 0;">+<span id="LC3472" class="line" lang="cpp"> <span class="p">}</span></span>
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3473
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<pre style="margin: 0;">+<span id="LC3473" class="line" lang="cpp"> <span class="p">}</span></span>
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3474
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<pre style="margin: 0;">+<span id="LC3474" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gene_level_counting</span><span class="p">)</span> <span class="p">{</span></span>
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3475
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<pre style="margin: 0;">+<span id="LC3475" 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;">ab_m_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Abundance_mat_gene</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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3476
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<pre style="margin: 0;">+<span id="LC3476" 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;">tpm_m_g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TPM_mat_gene</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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3477
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<pre style="margin: 0;">+<span id="LC3477" 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;">gc</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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3478
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<pre style="margin: 0;">+<span id="LC3478" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gc</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="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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3479
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<pre style="margin: 0;">+<span id="LC3479" class="line" lang="cpp"> <span class="n" style="color: #333;">ab_m_g</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">gc</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]});</span></span>
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3480
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<pre style="margin: 0;">+<span id="LC3480" class="line" lang="cpp"> <span class="n" style="color: #333;">tpm_m_g</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">({</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">gc_tpm</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]});</span></span>
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3481
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<pre style="margin: 0;">+<span id="LC3481" class="line" lang="cpp"> <span class="p">}</span></span>
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3482
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<pre style="margin: 0;">+<span id="LC3482" class="line" lang="cpp"> <span class="p">}</span></span>
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3483
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<pre style="margin: 0;">+<span id="LC3483" class="line" lang="cpp"> <span class="p">}</span></span>
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3484
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<pre style="margin: 0;">+<span id="LC3484" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Write plaintext abundances</span></span>
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3485
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<pre style="margin: 0;">+<span id="LC3485" class="line" lang="cpp"> <span class="n" style="color: #333;">plaintext_writer</span><span class="p">(</span><span class="n" style="color: #333;">abtsvfilename</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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3486
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<pre style="margin: 0;">+<span id="LC3486" 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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3487
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<pre style="margin: 0;">+<span id="LC3487" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gene_level_counting</span><span class="p">)</span> <span class="p">{</span></span>
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3488
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<pre style="margin: 0;">+<span id="LC3488" class="line" lang="cpp"> <span class="n" style="color: #333;">plaintext_writer_gene</span><span class="p">(</span><span class="n" style="color: #333;">gene_abtsvfilename</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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3489
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<pre style="margin: 0;">+<span id="LC3489" 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;">model</span><span class="p">);</span></span>
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3490
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<pre style="margin: 0;">+<span id="LC3490" class="line" lang="cpp"> <span class="p">}</span></span>
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3491
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<pre style="margin: 0;">+<span id="LC3491" class="line" lang="cpp"> <span class="p">}</span></span>
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3492
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<pre style="margin: 0;">+<span id="LC3492" class="line" lang="cpp"> </span>
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3493
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<pre style="margin: 0;">+<span id="LC3493" 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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isMatrixFile</span><span class="p">)</span> <span class="p">{</span></span>
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3494
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<pre style="margin: 0;">+<span id="LC3494" 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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3495
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<pre style="margin: 0;">+<span id="LC3495" 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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3496
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<pre style="margin: 0;">+<span id="LC3496" 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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3497
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<pre style="margin: 0;">+<span id="LC3497" 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;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seeds</span><span class="p">;</span></span>
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3498
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<pre style="margin: 0;">+<span id="LC3498" 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="n" style="color: #333;">s</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;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">B</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="p">{</span></span>
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3499
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<pre style="margin: 0;">+<span id="LC3499" class="line" lang="cpp"> <span class="n" style="color: #333;">seeds</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span> <span class="n" style="color: #333;">rand</span><span class="p">()</span> <span class="p">);</span></span>
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3500
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<pre style="margin: 0;">+<span id="LC3500" class="line" lang="cpp"> <span class="p">}</span></span>
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3501
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<pre style="margin: 0;">+<span id="LC3501" 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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3502
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<pre style="margin: 0;">+<span id="LC3502" 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="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;">B</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="p">{</span></span>
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3503
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<pre style="margin: 0;">+<span id="LC3503" class="line" lang="cpp"> <span class="n" style="color: #333;">Bootstrap</span> <span class="n" style="color: #333;">bs</span><span class="p">(</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;">index</span><span class="p">,</span> <span class="n" style="color: #333;">collection</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;">seeds</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">],</span> <span class="n" style="color: #333;">fl_means</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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3504
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<pre style="margin: 0;">+<span id="LC3504" 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;">"[bstrp] running EM for the bootstrap: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3505" 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">
3505
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<pre style="margin: 0;">+<span id="LC3505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bs</span><span class="p">.</span><span class="n" style="color: #333;">run_em</span><span class="p">();</span></span>
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3506
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<pre style="margin: 0;">+<span id="LC3506" 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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3507
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<pre style="margin: 0;">+<span id="LC3507" 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;">res</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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3508
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<pre style="margin: 0;">+<span id="LC3508" class="line" lang="cpp"> <span class="p">}</span></span>
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3509
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<pre style="margin: 0;">+<span id="LC3509" 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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3510
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<pre style="margin: 0;">+<span id="LC3510" class="line" lang="cpp"> <span class="p">}</span></span>
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3511
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<pre style="margin: 0;">+<span id="LC3511" class="line" lang="cpp"> <span class="p">};</span> <span class="c1" style="color: #998; font-style: italic;">// end of EM_lambda</span></span>
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3512
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<pre style="margin: 0;">+<span id="LC3512" class="line" lang="cpp"> </span>
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3513
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<pre style="margin: 0;">+<span id="LC3513" 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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<td class="new_line diff-line-num new" data-linenumber="3514" 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">
3514
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<pre style="margin: 0;">+<span id="LC3514" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nrow</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3515" 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">
3515
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<pre style="margin: 0;">+<span id="LC3515" 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="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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3516
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<pre style="margin: 0;">+<span id="LC3516" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">num_ids</span><span class="p">)</span> <span class="p">{</span></span>
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3517
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<pre style="margin: 0;">+<span id="LC3517" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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3518
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<pre style="margin: 0;">+<span id="LC3518" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nt</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;">min</span><span class="p">(</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="p">(</span><span class="n" style="color: #333;">num_ids</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">id</span><span class="p">));</span></span>
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3519
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<pre style="margin: 0;">+<span id="LC3519" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">first_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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3520
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<pre style="margin: 0;">+<span id="LC3520" 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;">nt</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="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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3521
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<pre style="margin: 0;">+<span id="LC3521" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</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="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="n" style="color: #333;">EM_lambda</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">));</span></span>
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3522
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<pre style="margin: 0;">+<span id="LC3522" class="line" lang="cpp"> <span class="p">}</span></span>
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3523
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<pre style="margin: 0;">+<span id="LC3523" 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;">nt</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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3524
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<pre style="margin: 0;">+<span id="LC3524" class="line" lang="cpp"> <span class="n" style="color: #333;">workers</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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3525
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<pre style="margin: 0;">+<span id="LC3525" class="line" lang="cpp"> <span class="p">}</span></span>
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3526
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<pre style="margin: 0;">+<span id="LC3526" class="line" lang="cpp"> <span class="p">}</span></span>
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3527
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<pre style="margin: 0;">+<span id="LC3527" 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;">" done"</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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3528
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<pre style="margin: 0;">+<span id="LC3528" class="line" lang="cpp"> </span>
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3529
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<pre style="margin: 0;">+<span id="LC3529" 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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3530
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<pre style="margin: 0;">+<span id="LC3530" class="line" lang="cpp"> </span>
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3531
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<pre style="margin: 0;">+<span id="LC3531" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="3532" 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">
3532
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<pre style="margin: 0;">+<span id="LC3532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isMatrixFile</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3533" 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">
3533
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<pre style="margin: 0;">+<span id="LC3533" class="line" lang="cpp"> <span class="n" style="color: #333;">writeSparseBatchMatrix</span><span class="p">(</span><span class="n" style="color: #333;">abfilename</span><span class="p">,</span> <span class="n" style="color: #333;">Abundance_mat</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="new_line diff-line-num new" data-linenumber="3534" 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">
3534
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<pre style="margin: 0;">+<span id="LC3534" class="line" lang="cpp"> <span class="n" style="color: #333;">writeSparseBatchMatrix</span><span class="p">(</span><span class="n" style="color: #333;">abtpmfilename</span><span class="p">,</span> <span class="n" style="color: #333;">TPM_mat</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="new_line diff-line-num new" data-linenumber="3535" 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">
3535
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<pre style="margin: 0;">+<span id="LC3535" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gene_level_counting</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3536" 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">
3536
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<pre style="margin: 0;">+<span id="LC3536" class="line" lang="cpp"> <span class="n" style="color: #333;">writeSparseBatchMatrix</span><span class="p">(</span><span class="n" style="color: #333;">gene_abfilename</span><span class="p">,</span> <span class="n" style="color: #333;">Abundance_mat_gene</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3537" 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">
3537
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<pre style="margin: 0;">+<span id="LC3537" class="line" lang="cpp"> <span class="n" style="color: #333;">writeSparseBatchMatrix</span><span class="p">(</span><span class="n" style="color: #333;">gene_abtpmfilename</span><span class="p">,</span> <span class="n" style="color: #333;">TPM_mat_gene</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">genes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3538" 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">
3538
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<pre style="margin: 0;">+<span id="LC3538" class="line" lang="cpp"> <span class="n" style="color: #333;">writeGeneList</span><span class="p">(</span><span class="n" style="color: #333;">genelistname</span><span class="p">,</span> <span class="n" style="color: #333;">model</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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3539
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<pre style="margin: 0;">+<span id="LC3539" class="line" lang="cpp"> <span class="p">}</span></span>
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3540
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<pre style="margin: 0;">+<span id="LC3540" class="line" lang="cpp"> <span class="p">}</span></span>
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3541
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<pre style="margin: 0;">+<span id="LC3541" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">calcEffLen</span><span class="p">)</span> <span class="p">{</span></span>
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3542
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<pre style="margin: 0;">+<span id="LC3542" class="line" lang="cpp"> <span class="n" style="color: #333;">writeFLD</span><span class="p">(</span><span class="n" style="color: #333;">fldfilename</span><span class="p">,</span> <span class="n" style="color: #333;">FLD_mat</span><span class="p">);</span></span>
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3543
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<pre style="margin: 0;">+<span id="LC3543" class="line" lang="cpp"> <span class="p">}</span></span>
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3544
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<pre style="margin: 0;">+<span id="LC3544" class="line" lang="cpp"> <span class="p">}</span></span>
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2398
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<td class="new_line diff-line-num" data-linenumber="3545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3545
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<pre style="margin: 0;"> <span id="LC3545" 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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2399
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3546
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<pre style="margin: 0;"> <span id="LC3546" 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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2400
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3547
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<pre style="margin: 0;"> <span id="LC3547" class="line" lang="cpp"> <span class="n" style="color: #333;">usagePseudo</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2429" style="width: 35px; color: rgba(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="3576" style="width: 35px; color: rgba(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">@@ -2429,14 +3576,22 @@ int main(int argc, char *argv[]) {</td>
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2429
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3576
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<pre style="margin: 0;"> <span id="LC3576" class="line" lang="cpp"></span>
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2430
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3577
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<pre style="margin: 0;"> <span id="LC3577" 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="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv_to_string</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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2431
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3578
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<pre style="margin: 0;"> <span id="LC3578" class="line" lang="cpp"></span>
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2432
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<pre style="margin: 0;">-<span id="LC2432" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="2433" 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">
2433
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<td class="new_line diff-line-num old" data-linenumber="3579" 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="LC2433" 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;">id</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;">id</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;">batchCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2434" 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">
2434
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<pre style="margin: 0;">-<span id="LC2434" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cc</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;">batchCounts</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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2435
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<pre style="margin: 0;">-<span id="LC2435" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">cc</span><span class="p">)</span> <span class="p">{</span></span>
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2436
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<td class="new_line diff-line-num old" data-linenumber="3579" 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="LC2436" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">first</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="p">{</span></span>
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2437
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<td class="new_line diff-line-num old" data-linenumber="3579" 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="LC2437" 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;">p</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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3579
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<pre style="margin: 0;">+<span id="LC3579" 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;">batch_bus</span><span class="p">)</span> <span class="p">{</span></span>
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3580
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<pre style="margin: 0;">+<span id="LC3580" 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;">id</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;">id</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;">batchCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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3581
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<pre style="margin: 0;">+<span id="LC3581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cc</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;">batchCounts</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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3582
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<pre style="margin: 0;">+<span id="LC3582" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">cc</span><span class="p">)</span> <span class="p">{</span></span>
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3583
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<pre style="margin: 0;">+<span id="LC3583" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">.</span><span class="n" style="color: #333;">first</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="p">{</span></span>
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3584
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<pre style="margin: 0;">+<span id="LC3584" 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;">p</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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3585
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<pre style="margin: 0;">+<span id="LC3585" class="line" lang="cpp"> <span class="p">}</span></span>
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3586
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<pre style="margin: 0;">+<span id="LC3586" 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;">p</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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2438
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3587
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<pre style="margin: 0;"> <span id="LC3587" class="line" lang="cpp"> <span class="p">}</span></span>
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2439
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<pre style="margin: 0;">-<span id="LC2439" 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;">p</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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3588
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<pre style="margin: 0;">+<span id="LC3588" class="line" lang="cpp"> <span class="p">}</span></span>
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3589
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<pre style="margin: 0;">+<span id="LC3589" 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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3590
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<pre style="margin: 0;">+<span id="LC3590" 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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3591
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<pre style="margin: 0;">+<span id="LC3591" 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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3592
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<pre style="margin: 0;">+<span id="LC3592" class="line" lang="cpp"> <span class="p">}</span></span>
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3593
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<pre style="margin: 0;">+<span id="LC3593" 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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3594
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<pre style="margin: 0;">+<span id="LC3594" 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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2440
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3595
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<pre style="margin: 0;"> <span id="LC3595" class="line" lang="cpp"> <span class="p">}</span></span>
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2441
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3596
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<pre style="margin: 0;"> <span id="LC3596" class="line" lang="cpp"> <span class="p">}</span></span>
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2442
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3597
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<pre style="margin: 0;"> <span id="LC3597" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2546" style="width: 35px; color: rgba(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="3701" style="width: 35px; color: rgba(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">@@ -2546,10 +3701,44 @@ int main(int argc, char *argv[]) {</td>
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2546
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3701
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<pre style="margin: 0;"> <span id="LC3701" 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="n" style="color: #333;">fldfilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fld.tsv"</span><span class="p">;</span></span>
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2547
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3702
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<pre style="margin: 0;"> <span id="LC3702" 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="n" style="color: #333;">genelistname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".genelist.txt"</span><span class="p">;</span></span>
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2548
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<td class="new_line diff-line-num" data-linenumber="3703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3703
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<pre style="margin: 0;"> <span id="LC3703" 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="n" style="color: #333;">genecountname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".genes.mtx"</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3704" 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">
3704
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<pre style="margin: 0;">+<span id="LC3704" 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="n" style="color: #333;">busbarcodelistname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".barcodes"</span><span class="p">;</span></span>
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3705
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<pre style="margin: 0;">+<span id="LC3705" 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="n" style="color: #333;">busoutputname</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;">output</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"/output.bus"</span><span class="p">;</span></span>
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2549
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3706
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<pre style="margin: 0;"> <span id="LC3706" class="line" lang="cpp"></span>
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2550
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<td class="new_line diff-line-num" data-linenumber="3707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3707
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<pre style="margin: 0;"> <span id="LC3707" class="line" lang="cpp"> <span class="n" style="color: #333;">writeECList</span><span class="p">(</span><span class="n" style="color: #333;">ecfilename</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>
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2551
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<td class="new_line diff-line-num" data-linenumber="3708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3708
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<pre style="margin: 0;"> <span id="LC3708" class="line" lang="cpp"> <span class="n" style="color: #333;">writeCellIds</span><span class="p">(</span><span class="n" style="color: #333;">cellnamesfilename</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">batch_ids</span><span class="p">);</span></span>
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2552
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<td class="new_line diff-line-num old" data-linenumber="3709" 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="LC2552" class="line" lang="cpp"> <span class="n" style="color: #333;">writeSparseBatchMatrix</span><span class="p">(</span><span class="n" style="color: #333;">tccfilename</span><span class="p">,</span> <span class="n" style="color: #333;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">ecmap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3709" 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">
3709
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<pre style="margin: 0;">+<span id="LC3709" 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_bus</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;">batch_bus_write</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3710" 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">
3710
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<pre style="margin: 0;">+<span id="LC3710" 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_bus_write</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3711" 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">
3711
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<pre style="margin: 0;">+<span id="LC3711" class="line" lang="cpp"> <span class="n" style="color: #333;">writeBUSMatrix</span><span class="p">(</span><span class="n" style="color: #333;">busoutputname</span><span class="p">,</span> <span class="n" style="color: #333;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">ecmap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3712" 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">
3712
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<pre style="margin: 0;">+<span id="LC3712" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3713" 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">
3713
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<pre style="margin: 0;">+<span id="LC3713" 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;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</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="new_line diff-line-num new" data-linenumber="3714" 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">
3714
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<pre style="margin: 0;">+<span id="LC3714" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write out fake barcodes that identify each cell</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3715" 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">
3715
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<pre style="margin: 0;">+<span id="LC3715" 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;">fake_bcs</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3716" 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">
3716
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<pre style="margin: 0;">+<span id="LC3716" class="line" lang="cpp"> <span class="n" style="color: #333;">fake_bcs</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3717" 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">
3717
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<pre style="margin: 0;">+<span id="LC3717" 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;">size_t</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;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</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="new_line diff-line-num new" data-linenumber="3718" 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">
3718
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<pre style="margin: 0;">+<span id="LC3718" class="line" lang="cpp"> <span class="n" style="color: #333;">fake_bcs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">binaryToString</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">BUSFORMAT_FAKE_BARCODE_LEN</span><span class="p">));</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3719" 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">
3719
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<pre style="margin: 0;">+<span id="LC3719" class="line" lang="cpp"> <span class="p">}</span></span>
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3720
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<pre style="margin: 0;">+<span id="LC3720" class="line" lang="cpp"> <span class="n" style="color: #333;">writeCellIds</span><span class="p">(</span><span class="n" style="color: #333;">busbarcodelistname</span><span class="p">,</span> <span class="n" style="color: #333;">fake_bcs</span><span class="p">);</span></span>
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3721
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<pre style="margin: 0;">+<span id="LC3721" class="line" lang="cpp"> <span class="p">}</span></span>
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3722
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<pre style="margin: 0;">+<span id="LC3722" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write out index:</span></span>
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3723
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<pre style="margin: 0;">+<span id="LC3723" class="line" lang="cpp"> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">write</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;">"/index.saved"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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3724
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<pre style="margin: 0;">+<span id="LC3724" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write out fragment length distributions if reads paired-end:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3725" 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">
3725
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<pre style="margin: 0;">+<span id="LC3725" 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;">single_end</span><span class="p">)</span> <span class="p">{</span></span>
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3726
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<pre style="margin: 0;">+<span id="LC3726" 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;">ofstream</span> <span class="n" style="color: #333;">flensout_f</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;">"/flens.txt"</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3727" 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">
3727
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<pre style="margin: 0;">+<span id="LC3727" 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;">size_t</span> <span class="n" style="color: #333;">id</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;">id</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;">batch_ids</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3728" 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">
3728
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<pre style="margin: 0;">+<span id="LC3728" 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;">fld</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;">batchFlens</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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3729
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<pre style="margin: 0;">+<span id="LC3729" 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;">size_t</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;">fld</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;">i</span> <span class="p">)</span> <span class="p">{</span></span>
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3730
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<pre style="margin: 0;">+<span id="LC3730" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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="p">{</span></span>
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3731
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<pre style="margin: 0;">+<span id="LC3731" class="line" lang="cpp"> <span class="n" style="color: #333;">flensout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span></span>
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3732
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<pre style="margin: 0;">+<span id="LC3732" class="line" lang="cpp"> <span class="p">}</span></span>
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3733
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<pre style="margin: 0;">+<span id="LC3733" class="line" lang="cpp"> <span class="n" style="color: #333;">flensout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">fld</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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3734
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<pre style="margin: 0;">+<span id="LC3734" class="line" lang="cpp"> <span class="p">}</span></span>
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3735
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<pre style="margin: 0;">+<span id="LC3735" class="line" lang="cpp"> <span class="n" style="color: #333;">flensout_f</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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3736
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<pre style="margin: 0;">+<span id="LC3736" class="line" lang="cpp"> <span class="p">}</span></span>
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3737
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<pre style="margin: 0;">+<span id="LC3737" class="line" lang="cpp"> <span class="n" style="color: #333;">flensout_f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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3738
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<pre style="margin: 0;">+<span id="LC3738" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="3739" 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">
3739
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<pre style="margin: 0;">+<span id="LC3739" 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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3740
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<pre style="margin: 0;">+<span id="LC3740" class="line" lang="cpp"> <span class="n" style="color: #333;">writeSparseBatchMatrix</span><span class="p">(</span><span class="n" style="color: #333;">tccfilename</span><span class="p">,</span> <span class="n" style="color: #333;">MP</span><span class="p">.</span><span class="n" style="color: #333;">batchCounts</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">.</span><span class="n" style="color: #333;">ecmap</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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3741
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<pre style="margin: 0;">+<span id="LC3741" class="line" lang="cpp"> <span class="p">}</span></span>
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2553
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3742
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<pre style="margin: 0;"> <span id="LC3742" 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;">pseudo_quant</span><span class="p">)</span> <span class="p">{</span></span>
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2554
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3743
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<pre style="margin: 0;"> <span id="LC3743" class="line" lang="cpp"> <span class="n" style="color: #333;">writeSparseBatchMatrix</span><span class="p">(</span><span class="n" style="color: #333;">abfilename</span><span class="p">,</span> <span class="n" style="color: #333;">Abundance_mat</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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2555
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3744
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<pre style="margin: 0;"> <span id="LC3744" class="line" lang="cpp"> <span class="n" style="color: #333;">writeFLD</span><span class="p">(</span><span class="n" style="color: #333;">fldfilename</span><span class="p">,</span> <span class="n" style="color: #333;">FLD_mat</span><span class="p">);</span></span>
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